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KING ABDULAZIZ UNIVERSITY
Faculty of Medicine
MEDICAL MICROBIOLOGY
Study Guide
Phase II, MBBS
2008
Faculty of Medicine
King Abdul-Aziz University
TABLE OF CONTENTS
Topic
Page
2
Welcome Letter
3-4
Lecture & Practical Topics
Third Year Courses
5
Structure of the module
6
Introduction
7
Aims & Objectives
8
Learning Resources
9
Course Evaluation
10
11-14
Faculty Listing
Icons
15
Topic Outlines
16
2
Faculty of Medicine
King Abdul-Aziz University
Welcome Letter
Dear Student,
Congratulations at successfully completing your second year in the Faculty of
Medicine and welcome to the third year and in particular to the Department of
Medical Microbiology.
This Microbiology Study Guide is intended as an aid during this course which is
taught during the third year in this faculty. It is not intended to be a complete
manual of Medical Microbiology but a guide to assist you throughout the course.
In this Study Guide you are provided with a clear description of the expectations,
contents, schedules and evaluation procedures used in the course. In addition, you
are provided with the essential basic microbiology information which you will be
able to refer to through out your career and which you will be able to supplement
during the year. This study guide is therefore, intended to be a working document,
which can be referred to and built on regularly.
This guide should also help you to communicate with members of the department
through out the period of study in this specialty. The course objectives listed here
are intended to help you become an independent and life-long learner. This is
essential requirement for those hoping to become and continue to be effective and
efficient physicians.
We hope you will find your study in this department interesting and would advice
you to use this opportunity to learn as much as possible about Medical
Microbiology as it is the main opportunity for you to be in close contact with this
medical specialty.
You will find members of this department very co-operative and accessible.
Please do not hesitate to contact us at any time.
Dr. Abdullah A. Al Ghamdi
Chairman, Department of Medical Microbiology
Phase II
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Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
LECTURES & PRACTICAL TOPICS
No
BACTERIOLOGY LECTURES
1
Introduction & General Bacteriology 1
2
General Bacteriology 2
3
Genetics & Genetic Engineering 1
4
Genetics & Genetic Engineering 2
5
Host-Parasite Relationships
6
Antibiotics & Chemotherapy
7
Staphylococci 1
8
Staphylococci 2
9
Streptococci and Enterococci 1
10
Streptococci and Enterococci 2
11
Neisseria 1
12
Neisseria 2
13
Gram-positive Rods 1
14
Gram-positive Rods 2
15
Gram-positive Rods 3
16
Gram-positive Rods 4
17
Mycobacteria 1
18
Mycobacteria 2
19
Gram-negative Rods 1
20
Gram-negative Rods 2
21
Gram-negative Rods 3
Phase II
4
STAFF
PAGE
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
22
Parvobacteria 1
23
Parvobacteria 2
24
Parvobacteria 3
25
Spirochaetes 1
26
Spirochaetes 2
27
Chlamydia, Rickettsia & Coxiella (1)
28
Chlamydia, Rickettsia & Coxiella (2)
29
Mycoplasma , Actinomyces & Nocardia
30
Mycology 1
31
Mycology 2
No
VIROLOGY LECTURES
32
General Virology 1
33
General Virology 2
34
Non-enveloped (Naked) DNA viruses
35
Enveloped DNA viruses 1
36
Enveloped DNA viruses 2
37
Enveloped DNA viruses 3
38
Hepatitis viruses
39
Non-enveloped (Naked) RNA viruses (1)
40
Non-enveloped (Naked) RNA viruses (2)
41
Enveloped RNA viruses 1
42
Enveloped RNA viruses 2
43
Rhabdoviruses and slow virus diseases
44
Arboviruses
45
Retroviruses and Oncogenesis
Phase II
5
STAFF
PAGE
Medical Microbiology
Faculty of Medicine
P#
King Abdul-Aziz University
PRACTICAL SESSIONS
1
Sterilisation & Disinfection
2
Microscopic Exam - Bacterial Growth & Metabolism
3
Laboratory Media, Isolation (Culture) & Sensitivity Testing
4
Gram-positive Cocci
5
Neisseria & Gram-positive Rods (1)
6
Gram-positive Rods (2)
7
Mycobacteria & Gram-negative Rods (1)
8
Gram-negative Rods (2) & Parvobacteria
9
Spirochaetes & Mycology
10
Virology
Phase II
6
STAFF
PAGE
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Third Year Courses
Semester V
Semester VI
Medical
Microbiology
Gastrointestinal
System
Medical
Pharmacology
Nutrition and
Metabolism
Endocrine
System
Early Clinical
Experience
&
Communication
Skills
Reproductive
System
Nervous System
Special Senses
Renal & Urinary
System
Islamic Studies
Medical Ethics
Arabic Language
Islamic Studies
STRUCTURE OF THE MODULE
TIMETABLED HOURS:
45 Lectures
10 Practicals
TEACHING DEPARTMENT:
Medical Microbiology
Phase II
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Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Introduction
The Medical Microbiology course has been designed to give third year medical
students valuable knowledge concerning the medical relevance of microorganisms. It is made up of three parts comprising bacteriology, mycology and
virology.
The first part includes general and systematic bacteriology. "General
Bacteriology" describes the morphology, structure, growth, metabolism and
genetics of bacteria. Antibiotics and chemotherapy, sterilisation and disinfection
are also discussed. The "Systemic Bacteriology" outlines the characters of microorganisms which are medically important including modes of transmission and
pathogenesis, laboratory diagnosis, treatment, prevention and control of various
infections caused by them.
The second part, “Mycology”, describe medically important fungi and fungal
diseases in terms of modes of transmission and pathogenesis, laboratory
diagnosis, antifungal treatment, prevention and control.
The third part includes general and systemic virology. “General Virology”
describes the morphology, structure, and multiplication cycle of viruses.
Antiviral agents are also discussed. The "Systemic Virology" outlines the
characters of viruses which are medically important including; modes of
transmission and pathogenesis, laboratory diagnosis, treatment, prevention and
control of various infections caused by them.
Practical sessions are closely related to the lecture topics to enable students to
experience Clinical and Diagnostic Microbiology.
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Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
AIMS & OBJECTIVES
At the end of the course the student will:
 Become oriented with basic structure of different types of micro-organisms
with medical relevance, their characters, mode of transmission and
pathogenesis of different diseases.
 Be acquainted with various methods of sterilization and disinfection.
 Be familiar with the mechanism of action of antimicrobial agents and how
micro-organisms develop resistance to them.
 Understand basic laboratory tests and be able to interpret them
 Be able to suggest treatment and prophylaxis for each infectious disease
studied.
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Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
LEARNING RESOURCES
The following textbooks are recommended for students throughout the course.
These texts are available in the College library for reference and all are available in
medical book shops locally (Shugery, Medical Book Center, Mars, Khazindar and
Jarir).
Title
Microbiology
Medical Microbiology
Medical Microbiology
Medical Microbiology
Author
Harvey
Murray
Jawetz
Mims
Publisher
Lippincott
ASM Press
McGraw Hill
Mosby
ISBN
0781782155
9781555813710
0071412077
0323035752
 It is the students own responsibility to take notes during the lecture and to
make their own lecture notes while referring to standard texts.
 Students are expected to refer to recommended texts for each topic covered
since the lecture time may not allow a detailed review into each topic.
 Examination questions are referred to the standard recommended textbooks
Phase II
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Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
COURSE EVALUATION
Students performance will be evaluated by:
Continuous assessment –
(Quizzes and laboratory work through out the year)
Mid-year examination -
15%
25%
Final examination
(Includes Written exam 45% of total final mark and
OSPE 15% of total final work)
60%
Grading is based on the cumulative of all types of evaluation mentioned
above. A minimum of 60% of the total mark should be achieved for passing the
course. The grades given are:
Excellent , Very good, Good , Satisfactory and Fail.
Students are required to attend all lectures, tutorials and practical classes.
Attendance is recorded and students who are frequently absent without an
official notification will not be allowed to enter the exams.
Phase II
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Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
FACULTY LISTING
A: MALE SECTION
Name
ROOM#
PHONE#
E-MAIL
Dr. Abdullah A. Al Ghamdi
Associate Professor
Chairman
1/964
21122
AAAAlghamdi
@hotmail.com
Prof. Nashaat A. Ismail
Professor
1/963
21123
nismail@
kaau.edu.sa
Prof. Hassan El Banna
Professor
1/932
21117
Dr. Sulaiman M. Al-Ansari
Associate Professor
1/933
21180
Dr. Asif A. Jiman-Fatani
Assistant Professor
1/952
21083
afatani@
maktoob.com
Mr. Mohammed S. Banaja
Demonstrator
(On leave for postgraduate
studies)
anwar_mt@
hotmail.com
Mr. Anwar M. Hashim
Demonstrator
(On leave for postgraduate
studies)
Mr. Shadi Zakai
Demonstrator
(On leave for postgraduate
studies)
Phase II
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Medical Microbiology
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King Abdul-Aziz University
Technical Staff
Male Section
Name
ROOM#
PHONE#
E-MAIL
Mr. Mohammed I. Sheikh
Technician
1/953
21081
mihassan@
kaau.edu.sa
Mr. Mahmoud S. Salem
Technician
1/930
21082
mahmoud_salem3
@hotmail.com
Mr. Hani Abdallah Yousef
Technician
1/910
21120
Mr. Sameer S. Masrahi
Technician
1/930
21115
Phase II
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Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
B: FEMALE SECTION
Name
ROOM#
PHONE#
Dr. Razina M. Q. Zaman
Associate Professor
Co-ordinator of Female Section
1/ 511
Prof. Mervat M. AbdEl-Hady
Professor
1/ 512
24083
mervatelhady
@yahoo.com
Dr. Eman K. Al Digs
Assistant Professor
1/ 550
24092
dremanbiology
@hotmail.com
Dr. Amal Fathallah
Associate Professor
1/612
24091
AmalFM@
Hotmail.com
Ms. Balgees A. Al Maeena
Lecturer
1/ 620
24094
Balgees2004@
Yahoo.com
Ms. Nuha A. Jumaa
Demonstrator
(On leave for postgraduate studies)
1/ 551
Ms. Manal A. Zubair
Demonstrator
1/616
Ms. Taghreed Y. Jamal
Demonstrator
1/616
24084
E-MAIL
razinazaman
@hotmail.com
24093
Manal_zubair@
Yahoo.com
Dr Noora Daffa
Demonstrator
(On leave for postgraduate studies)
Dr Maha Allawi
Demonstrator
(On leave for postgraduate studies)
Phase II
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Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Technical Staff
Female Section
Name
Ms. Salwa Al Goaly
Technician
ROOM#
1/ 621
PHONE#
24088
24153
E-MAIL
Salwass@
yahoo.com
Ms. Fatma Al Sharif
Technician
1/531
24089
tofy_3000@
yahoo.com
Ms. Nahdah Al-Shammrei
Technician
1/530
24090
Alshammari_Nana@
Yahoo.com
Ms. Rana Baghalaf
Technician
1/510
24002
Ferrari_rrr444@
Hotmail.com
Phase II
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Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Icons
(standards)
The following icons have been used to help you identify the various experiences
you will be exposed to.
Learning objectives
Content of the lecture
Independent learning from textbooks
Self- Assessment (the answer to self-assessment exercises will be
discussed in tutorial sessions)
The main concepts
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Medical Microbiology
Faculty of Medicine
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Topic Outlines
Phase II
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Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Lectures 1- 2: Introduction & General Bacteriology
Department: Medical Microbiology
Lecturer:
At the end of the lecture you should be able to:
1) Recognise the role of Microbiology in Disease.
2) Differentiate between prokaryotes & eukaryotes.
3) Describe bacterial cell structures & their
functions.
4) Differentiate between Gram-positive & Gramnegative bacteria.
5) Describe the general types of bacterial
morphology.
6) Describe bacterial growth requirements.
7) Describe the bacterial growth cycle.
Microbiology involves a study of bacteria and
viruses. Bacteria and viruses differ in their
characteristics and differ from eukaryotic cells.
Diagram of bacterial cell structure shows the
organelles and their functions. Cell wall structure of
Gram-positive and Gram-negative bacteria shows
the difference between these two main groups of
bacteria. Bacterial cell morphology is used in
classification of bacterial groups. Bacteria are
divided into different groups according to their
oxygen requirement, nutritional requirement and
optimal growth temperatures. A one-step growth
curve shows the stages in bacterial growth.
(Insert here handouts and additional
Bacterial cells have essential and non-essential pages for notes if needed)
cell structures. Some components act as
Phase II
Medical Microbiology
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Faculty of Medicine
King Abdul-Aziz University
virulence factors for the bacteria.

Microbiology by Harvey, Champe and
Fisher. Second Edition (2007). Publisher:
Lippincott Williams & Wilkins

Jawetz, Melnick & Adelbergs Medical
Microbiology.
Self-assessment
Briefly answer the following short questions:
1-Gram-negative bacterial cell is characterised
by:
abcd2- Enumerate essential structures of the bacterial
cell and give one function of each one.
Phase II
19
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Lectures 3 & 4: Genetics & Genetic Engineering
Department: Medical Microbiology
Lecturer:
At the end of the lecture you should be able to:
1) Discuss microbial gene structure and function.
2) Differentiate between phenotypic and genotypic
variation.
3) Define different types of mutations.
4) Describe and discuss the methods of gene transfer
in bacteria.
5) Describe the structure, life cycle(s) and uses of
bacteriophages.
6) Define and describe extra-chromosomal genetic
material (plasmids and transposons).
7) Discuss the process of genetic engineering and its
applications.
Genetic material in a bacterial cell is not bound by
nuclear membrane and is a single long
chromosome which codes for all the essential
genetic information.
Bacterial cells may show variation which can be
reversible and temporary or irreversible and
permanent. Bacteria may carry out gene transfer by
either
transformation,
transduction
or
conjugation. Bacteriophages, plasmids and
transposons are important tools in gene transfer.
Genetic engineering is a very effective technique
which is widely applied in diagnostic microbiology,
preparation of vaccines and other important
(Insert here handouts and additional
substances. The basis of molecular biology
techniques involves the use important enzymes, pages for notes if needed)
namely restriction endonucleases and ligases.
Phase II
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Faculty of Medicine
King Abdul-Aziz University
Definitions of different types of mutations are
important. The differences between the three
methods of gene transfer is essential and students
must be able to establish which method is the most
efficient and also on mechanisms which are common
in nature and those which are used mostly as
laboratory techniques.

Microbiology by Harvey, Champe and
Fisher. Second Edition (2007). Publisher:
Lippincott Williams & Wilkins

Jawetz, Melnick & Adelbergs Medical
Microbiology.
Self-assessment
MCQ:
1)Transduction is the transfer of DNA through:
A- Sex pilus.
B- Plasmids.
C- Transposons.
D- Bacteriophage.
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Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Lecture 5: Host-Parasite Relationships
Student Notes:
.
Department: Medical Microbiology
Lecturer: Teaching Staff
At the end of the lecture you should be able to:
1.
Understand
the
definitions
of:
Saprophytes – Parasites – Normal Flora
(Commensal) – Infection – Virulence
Factors – Transmission – Intracellular
Survival - Toxigenicity
2.
Know the normal flora of the human
body, the areas colonized, their
importance, and the potential for
infection
3.
Know the methods employed by microorganisms that cause infection
4.
Understand infection as a biological
process comprising a series of stages
5.
Differentiate
between
bacterial
endotoxins & exotoxins (with some
examples)

The reason why some organisms can
peacefully coexist with humans while others
go on to produce disease lies in the nature of
the interaction between microbe and host.

Much is learnt in recent years about
mechanisms of microbial disease, especially at
a molecular level.


Knowledge of these process is necessary to
understand how to diagnose, treat, and prevent
infection effectively.
Pathogenic bacteria produce a variety of
virulence factors
(Insert here handouts and additional
pages for notes if needed)
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Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Continue … Lecture 5: Host-Parasite Relationships
Student Notes:
.
Microbiology by Harvey, Champe and
Fisher , Second Edition (2007).
Publisher: Lippincott Williams &
Wilkins
In the computer cluster also you have the
opportunity to see some useful web sites about the
infectious diseases. We would recommend you to
use the key word – Infection – in the search engine
google (www.google.com). Don’t read any details at
this stage. Later in the course, we will direct you to
specific useful sites.
Other websites:
 http://www.kcom.edu/faculty/chamberlain
Self-assessment
MCQ:
The predominant bacterial species that colonizes
the human skin is:
A. Lactobacillus
B. Streptococcus pneumoniae
C. Staphylococcus epidermidis
D. Bacteroides fragilis
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Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Lecture 6: Antimicrobial Chemotherapy
Department: Medical Microbiology
Lecturer:
Student Notes:
.
At the end of the lecture you should be able to:
1) Define and discuss the terms antibiotic,
bactericidal, bacteriostatic, narrow spectrum and
broad spectrum.
2) Describe the characteristics of certain drugs that
make them suitable as chemotherapeutic agents.
3) Describe the main mechanisms of action of
antibiotics.
4) List chemotherapeutic agents that are inhibitors of
cell wall synthesis, cytoplasmic membrane function,
protein synthesis and cell metabolism.
5) Discuss methods by which micro-organisms are
able to develop resistance to antimicrobials.
6) Discuss mechanisms which may be used to reduce
bacterial resistance.
7) Describe complications of anti-microbial agents.
The advent of antimicrobial agents has had a
tremendous effect on infectious diseases and the
range of diseases that can be cured and prevented is
constantly expanding. Chemotherapeutic agents
must be safe for use in the host and must have
specific site of action. Combinations of antibiotics
may be used in order to broaden the antibacterial
spectrum and to prevent the emergence of resistance
for some diseases. In some cases this may also give
a synergistic killing effect. Some antibiotics may
have antagonistic effects where the activity of one
antibiotic may interfere with the activity of another.
Phase II
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Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Beta-lactamase enzymes produced by bacteria
hydrolyse the beta-lactam ring found in the penicillin
and cephalosporin group of antibiotics.
The most common mechanism of antibiotic activity
is interference with bacterial cell wall synthesis.
Most of the cell wall active antibiotics are classified
as beta-lactam antibiotics. Some other antibiotics
may also effect bacterial cell wall synthesis such as
Vancomycin or Bacitracin as well as some antimycobacterial agents. Familiarity with the main
classes of antibiotics is required including examples
of agents which belong to each different classes and
their respective mode of action.

Microbiology by Harvey, Champe and
Fisher. Second Edition (2007). Publisher:
Lippincott Williams & Wilkins

Jawetz, Melnick & Adelbergs Medical
Microbiology.
Self-assessment
Briefly answer the following short question:
1-Properties of an ideal antimicrobial agent are:
abcd-
Phase II
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Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Lecture 7: Staphylococci (1)
Student Notes:
.
Department: Medical Microbiology
Lecturer: Teaching Staff
At the end of the lecture you should be able to:
1. Describe the general characteristics of the
genus Staphylococcus
2. Differentiate between Staphylococcus and
other Gram positive cocci.
3. Epidemiology of Staph. aureus
4. Describe how to identify Staph. aureus
5. Know virulence factors of Staph. aureus
6. Describe diseases caused by Staph. aureus
Description of staphylococci and the three main
species. Features of Staph aureus. Virulence factors:
Toxins and enzymes. Diseases cased by Staph.
aureus : Suppurative infections & toxin-mediated
diseases.
Remember, the three main species
Staphylococcus.
Staph. aureus is the most virulent species
of
(Insert here handouts and additional
pages for notes if needed)
Phase II
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Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Continue … Lecture 7: Staphylococci (1)
Student Notes:
.
Microbiology by Harvey, Champe and
Fisher , Second Edition (2007).
Publisher: Lippincott Williams &
Wilkins
In the computer cluster also you have the
opportunity to see some useful web site about the
staphylococci but these should not used in isolation.
We would recommend you look at the following
web sites:
http://www.cdc.gov
http://www.who.int
http://www.medicinenet.com/staph_infection/article.
htm
http://www.elon.edu/shouse/physiology/physiol22/Lectur
e14.html
Self-assessment
Answer the following short question:

Mention diseases caused by Staph. aureus?
Phase II
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Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Lecture 8: Staphylococci (2)
Department: Medical Microbiology
Lecturer: Teaching Staff
Student Notes:
.
At the end of the lecture you should be able to:
1. Discuss the laboratory diagnosis of Staph.
aureus.
2. Describe the typing tests of Staph. aureus.
3. Know antimicrobial treatment of infections
caused by Staph. aureus.
4. Describe briefly treatment and control of
staphylococcal infections and explain how
resistance is a serious clinical problem.
5. Know the increasing importance of coagulase
negative Staphylococci as causative agents of
infections.
6. Know common infections caused by Staph.
epidemmdis and its virulence factors (eg
slime layer).
7. Know the
laboratory diagnosis
&
management of infections caused by Staph.
epidemmdis.
8. Describe features and the disease (urinary
tract
infection)
caused
by
Staph.
saprophyticus.




Laboratory diagnosis includes: types of
specimens,
microscopy,
culture,
confirmatory tests.
Typing tests are important in hospital crossinfection investigations to trace for possible
source(s) and to know the routes if
infections.
Staph. aureus strains could be resistant to
many antimicrobials eg MRSA (methicillinresistant Staph. aureus).
Features of Staph. epidermidis and Staph.
saprophiticus will be mentioned.
Remember the diseases caused by the three (Insert here handouts and additional
species of Staphylococcus
pages for notes if needed)
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Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Continue … Lecture 8: Staphylococci (2)
Student Notes:
.
Microbiology by Harvey, Champe and
Fisher , Second Edition (2007).
Publisher: Lippincott Williams &
Wilkins
In the computer cluster also you have the
opportunity to see some useful web site about the
staphylococci but these should not used in isolation.
We would recommend you look at the following
web sites:
http://www.cdc.gov
http://www.who.int
http://www.medicinenet.com/staph_infection/article.
htm
http://www.elon.edu/shouse/physiology/physiol22/Lectur
e14.html
Self-assessment
Answer the following short question:

Mention diseases caused by staphylococci,
laboratory diagnosis and treatment.
Phase II
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Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Lecture 9: Streptococci & Enterococci (1)
Student Notes:
.
Department: Medical Microbiology
Lecturer: Teaching Staff
At the end of the lecture you should be able to:
1. Describe the general characteristics of the
genus Streptococcus
2. Know the classifications of streptococci.
3. Discuss the importance of haemolysis
patterns on the blood agar in the
identification of streptococcal isolates.
4. Explain the Lancefield classification of the
Streptococci.
5. Know the features of Streptococcus pyogenes
6. Describe the pathogenesis, virulence factors
of Strep. pyogenes..
7. Describe the clinical diseases associated with
Strep. pyogenes.
8. Know the laboratory diagnosis, treatment,
and control of Group A streptococcal
diseases.






Description of streptococci (microscopy).
Classification according to the types of
haemolysis.
Lancefield classification of beta-haemolytic
streptococci.
Pathogenesis and virulence factors of Strep.
pyogenes.
Diseases caused by Strept. pyogenes:
suppurative infections, post-streptococcal
diseases, and toxin-mediated diseases.
Treatment and prevention

The features & classifications of
streptococci.
 Features, pathogenesis, virulence factors,
(Insert here handouts and additional
diseases, diagnosis, and treatment of
infections/diseases caused by Strept. pages for notes if needed)
pyogenes.
Phase II
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Faculty of Medicine
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Continue … Lecture 9: Streptococci & Enterococci (2)
Student Notes:
.
Microbiology by Harvey, Champe and
Fisher , Second Edition (2007).
Publisher: Lippincott Williams &
Wilkins
In the computer cluster also you have the
opportunity to see some useful web sites about the
streptococci. We would recommend you look at the
following web sites:
http://www.cdc.gov
http://www.who.int
Self-assessment
Answer the following short question:

Mention diseases
pyogenes?
Phase II
caused
by
Strep.
31
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Lecture 10: Streptococci & Enterococci (2)
Student Notes:
.
Department: Medical Microbiology
Lecturer: Teaching Staff
At the end of the lecture you should be able to:
1. Describe Strept. agalactiae and its
epidemiology,
associated
infections,
laboratory diagnosis, and treatment
2. Describe Strept. pneumoniae in terms of
morphology, epidemology, virulence factors,
diseases, treatment, and prevention.
3. Describe the general characteristics of
viridans streptococci in terms of morphology,
epidemiology,
pathogenecity,
diseases,
treatment and prevention.
4. Discuss the general characteristics of the
enterococci in terms of morphology,
epidemiology,
pathogenecity,
diseases,
treatment and prevention.
5. Describe the general characteristics of the
anaerobic streptococci





Description of S. agalactiae (group B
streptococcus) and its epidemiology
GBS-associated infections in neonates and
adults.
Description of S. pneumoniae
and its
epidemiology, virulence factor, associated
infections,
diagnosis,
treatment
and
prevention
Description of viridans streptococci and their
epidemiology,
pathogenesis,
associated
infections/diseases, diagnosis, treatment and
prevention
Description of enterococci and their
epidemiology,
pathogenesis,
associated
infections/diseases, diagnosis, treatment and
prevention
Remember beta & alpha-haemolytic streptococci –
(Insert here handouts and additional
enterococci
pages for notes if needed)
Phase II
32
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Continue … Lecture 10: Streptococci & Enterococci (2)
Student Notes:
.
Microbiology by Harvey, Champe and
Fisher , Second Edition (2007).
Publisher: Lippincott Williams &
Wilkins
In the computer cluster also you have the
opportunity to see some useful web site about the
streptococci and enterococci. We would recommend
you look at the following web sites:
http://www.cdc.gov
http://www.who.int
Self-assessment
Answer the following short question:

Mention diseases caused by Streptococcus
pneumoniae?
Phase II
33
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Lecture 11: Neisseria (1)
Student Notes:
.
Department: Medical Microbiology
Lecturer: Teaching Staff
At the end of the lecture you should be able to:
1. Describe the properties of Neisseria
2. Describe the causative agent of
meningococcal (epidemic) meningitis, and
discuss its epidemiology, pathogenesis,
clinical diseases, virulence factors, laboratory
diagnosis, antimicrobial chemotherapy,
prevention, and prophylaxis.



Description of Neisseria
Meningococcal meningitis: Epidemiology,
Pathogenesis, Clinical Features,
Lab
diagnosis, Treatment, Vaccination, Antibiotic
prophylaxis
Meningococcaemia


Meningococcal meningitis
Meningococcaemia
(Insert here handouts and additional
pages for notes if needed)
Phase II
34
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Continue … Lecture 11: Neisseria (1)
Student Notes:
.
Microbiology by Harvey, Champe and
Fisher , Second Edition (2007).
Publisher: Lippincott Williams &
Wilkins
In the computer cluster also you have the
opportunity to see some useful web sites about the
N. meningitides and meningococcal meningitis. We
would recommend you look at the following web
sites:
http://www.cdc.gov
http://www.who.int
Self-assessment
Answer the following short question:

Mention diseases caused by different species
of Neisseria?
Phase II
35
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Lecture 12: Neisseria (2)
Student Notes:
.
Department: Medical Microbiology
Lecturer: Teaching Staff
At the end of the lecture you should be able to:
1. Describe the causative agent of gonorrhea.
2. Discuss its epidemiology, pathogenesis,
clinical diseases and chemotherapy.
3. Discuss the laboratory diagnosis of Neisseria
gonorrhoeae infections.


Diseases caused by N. gonorrhoeae in men,
women, and neonates
Laboratory diagnosis, Treatment and
Prevention


Gonococcal cervicitis & urethritis
Ophthalmia neonatorum
(Insert here handouts and additional
pages for notes if needed)
Phase II
36
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Continue … Lecture 12: Neisseria (2)
Student Notes:
.
Microbiology by Harvey, Champe and
Fisher , Second Edition (2007).
Publisher: Lippincott Williams &
Wilkins
In the computer cluster also you have the
opportunity to see some useful web sites about N.
gonorrheae and gonococcal diseases. We would
recommend you look at the following web sites:
http://www.cdc.gov
http://www.who.int
Self-assessment
Answer the following short question:


Mention diseases caused by N. gonorrheae ?
Discuss the laboratory diagnosis of
gonococcal diseases
Phase II
37
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Lecture 13: Gram-positive Rods (1)
Student Notes:
.
Department: Medical Microbiology
Lecturer: Teaching Staff
At the end of the lecture you should be able to:
1. Describe the general characteristics of the
spore-forming and the non spore-forming
GPR
2. Understand the clinical significance
of spores, their structure, and how to
destroy them.
3. Describe the general characteristics of
the genus Bacillus.
4. Describe
the
epidemiology,
pathogenesis and clinical infections
associated with Bacillus anthracis &
Bacillus cereus.
5. Discuss laboratory diagnosis and
treatment of Bacillus anthrcis &
Bacillus cereus infections.
 Aerobic spore-forming GPR
 Spores
 Autoclaving
 Bacillus anthracis & anthrax
 B. cereus food poisoning
diarrhoeal)
(emetic
&
Spores – autoclaving – anthrax – biological
weapons - B. cereus food poisoning
(Insert here handouts and additional
pages for notes if needed)
Phase II
38
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Continue … Lecture 13: Gram-positive Rods (1)
Student Notes:
.
Microbiology by Harvey, Champe and
Fisher , Second Edition (2007).
Publisher: Lippincott Williams &
Wilkins
In the computer cluster also you have the
opportunity to see some useful web sites about B.
anthracis and anthrax. We would recommend you
look at the following web sites:
http://www.cdc.gov
http://www.who.int
Self-assessment
Answer the following short question:

Describe the causative agent of anthrax.
Discuss its pathogenesis, clinical features,
laboratory diagnosis, and treatment.
Phase II
39
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Lecture 14: Gram-positive Rods (2)
Student Notes:
.
Department: Medical Microbiology
Lecturer: Teaching Staff
At the end of the lecture you should be able to:
1. Describe the general characteristics of the
anaerobic spore-forming GPR
2. Describe the general characteristics of
the genus Clostridium.
3. Discuss
the
epidemiology,
pathogenesis,
clinical
feature,
laboratory diagnosis, treatment, and
prevention of tetanus.
4. Discuss
the
epidemiology,
pathogenesis,
clinical
feature,
laboratory diagnosis, treatment, and
prevention of botulism.




Anaerobic spore-forming GPR
C. tetani & tetanus
C. botulinum & botulism
C. botulinum toxin as a biological weapon



Anaerobic Anaerobic spore-forming GPR
Tetanus
Botulism
(Insert here handouts and additional
pages for notes if needed)
Phase II
40
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Continue … Lecture 14: Gram-positive Rods (2)
Student Notes:
.
Microbiology by Harvey, Champe and
Fisher , Second Edition (2007).
Publisher: Lippincott Williams &
Wilkins
In the computer cluster also you have the
opportunity to see some useful web sites about
tetanus and botulism. We would recommend you
look at the following web sites:
http://www.cdc.gov
http://www.who.int
Self-assessment
Answer the following short question:

Describe the causative agent of tetanus.
Discuss its pathogenesis, clinical features,
laboratory diagnosis, treatment, and
prevention

Describe the causative agent of botulism.
Discuss its pathogenesis, clinical features,
laboratory diagnosis, treatment, and
prevention
Phase II
41
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Lecture 15: Gram-positive Rods (3)
Student Notes:
.
Department: Medical Microbiology
Lecturer: Teaching Staff
At the end of the lecture you should be able to:
1. Describe
the
epidemiology,
pathogenesis, virulence factors, and
diseases
associated
with
C.
perferingens.
2. Discuss
the
transmission,
pathogenesis,
clinical
features
prevention of gas gangrene caused by
C. perferingens.
3. Discuss
the
transmission,
pathogenesis,
clinical
features,
laboratory diagnosis, treatment, and
prevention of food poisoning caused
by C. perferingens.
4. Discuss
the
transmission,
pathogenesis,
clinical
features,
laboratory diagnosis, treatment, and
prevention of diseases caused by C.
difficile.




C. perferengens: Epidemiology, Virulence
factors, Diseases (gas gangrene, cellulites,
and food poisoning)
C. perferengens gas gangrene: transmission,
pathogenesis, clinical findings, laboratory
diagnosis, treatment, and prevention.
C.
perferengens
food
poisoning:
transmission, pathogenesis, clinical findings,
laboratory
diagnosis,
treatment,
and
prevention.
C.
difficile:
Diseases,
Transmission,
Pathogenesis,
Clinical
findings,
Lab
diagnosis, Treatment, and Prevention
(Insert here handouts and additional
pages for notes if needed)
Phase II
42
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Continue … Lecture 15: Gram-positive Rods (3)
Student Notes:


.
Diseases caused by C. perferengens : gas
gangrene, cellulites, and food poisoning
Diseases caused by C. difficile : diarrhoea
and pseudomembranous colitis
Microbiology by Harvey, Champe and
Fisher , Second Edition (2007).
Publisher: Lippincott Williams &
Wilkins
In the computer cluster also you have the
opportunity to see some useful web sites about C.
peferingens and C. difficile. We would recommend
you look at the following web sites:
http://www.cdc.gov
http://www.who.int
Self-assessment
Answer the following short question:
 List the major species of Clostridium and the
disease they caused in humans.
 Explain the mechanism of action of the
Clostridial infection.
 Discuss laboratory diagnosis of Clostrial
infections.
 Describe
the
causative
agent
of
pseudomembranous colitis, its pathogenesis,
clinical findings, laboratory diagnosis,
treatment, and prevention
Phase II
43
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Lecture 16: Gram-positive Rods (4)
Student Notes:
.
Department: Medical Microbiology
Lecturer: Teaching Staff
At the end of the lecture you should be able to:
1. Discuss the non spore-forming GPR
2. Describe the properties,
epidemiology, transmission,
pathogenesis, virulence factors, and
diseases associated with
Corynebacterium diphtheriae.
3. Discuss the laboratory diagnosis,
treatment, and prevention of
diphtheria (respiratory diphtheria)
4. Understand the cutaneous diphtheria
5. Describe the properties,
epidemiology, transmission,
pathogenesis, virulence factors, and
diseases associated with Listeria
monocytogenes.
6. Discuss the laboratory diagnosis,
treatment, and prevention of diseases
associated with Listeria
monocytogenes.





Corynebacterium diphtheriae: Properties
Diphtheria: Transmission, Pathogenesis,
Clinical findings, Laboratory diagnosis,
Treatment, and Prevention
Cutaneous Diphtheria
Listeria monocytogenes : Properties,
Pathogenesis, Virulence factors, Associated
diseases in neonates, adults, pregnant
women, and immunocompromised patients
Laboratory diagnosis, Treatment, and
Prevention of diseases caused by Listeria
monocytogenes
(Insert here handouts and additional
pages for notes if needed)
Phase II
44
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Continue … Lecture16: Gram-positive Rods (4)
Student Notes:


.
Diseases caused by C. diphtheriae :
Respiratory & Cutaneous Diphtheria
Diseases caused by L monocytogenes :
Meningitis
in
neonates
and
immunocompromised patients.
Microbiology by Harvey, Champe and
Fisher , Second Edition (2007).
Publisher: Lippincott Williams &
Wilkins
In the computer cluster also you have the
opportunity to see some useful web sites about
diphtheria. We would recommend you look at the
following web sites:
http://www.cdc.gov
http://www.who.int
Self-assessment
Answer the following short question:
 Describe the causative agent of diphtheria
and discuss its pathogenesis, clinical
findings, laboratory diagnosis, treatment,
and prevention
Phase II
45
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Lecture 17: Mycobacteria (1)
Department: Medical Microbiology
Lecturer: Teaching Staff
Student Notes:
.
At the end of the lecture you should be able to:
1.
Relate
the
structure
of
the
mycobacterial cell wall to the property
of acid fastness.
2.
List the main Mycobacterial species
associated with tuberculosis and
leprosy.
3.
Recognize the impact of TB on health
of mankind.
4.
Discuss the epidemiology, virulence
factors,
pathogenesis,
primary
infection, secondary (reactivation)
infection TB
5.
Relate the recent rise of TB to the
AIDS epidemic.
6.
Discuss the pulmonary & extrapulmonary TB
7.
Understand the military TB
8.
Discuss the laboratory diagnosis of TB
9.
Understand the tuberculin skin test








Description of Mycobacteria
Features of the cell wall
Mycobaterial species that infect humans (eg
M. tuberculosis, M. bovis, M. africanum, M.
avium complex & M. leprae)
M. tuberculosis/TB: epidemiology, virulence
(eg, cell wall & cord factor), pathogenesis,
primary infection, secondary (reactivation or
post-primary) infection.
Clinical features of pulmonary TB
Extra-pulmonary
TB
(cervical
lymphadenopathy, renal TB, TB meningitis,
etc).
Lab Diagnosis: Specimens, Microscopy
(Ziehl-Neelsen & auramine phenol stains),
Culture and its duration (on LewensteinJensen & other special liquid media), PCR
(Insert here handouts and additional
Mantoux (tuberculin) skin test
pages for notes if needed)
Phase II
46
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Continue … Lecture 17: Mycobacteria (1)
Student Notes:


.
Features of Mycobacteria
Pulmonary & extrapulmonary TB
Microbiology by Harvey, Champe and
Fisher , Second Edition (2007).
Publisher: Lippincott Williams &
Wilkins
In the computer cluster also you have the
opportunity to see some useful web sites about TB.
We would recommend you look at the following
web sites:
http://www.cdc.gov
http://www.who.int
Self-assessment
Answer the following short question:
 Discuss the clinical features, laboratory
diagnosis, and treatment of pulmonary TB.
Phase II
47
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Lecture 18: Mycobacteria (2)
Student Notes:
.
Department: Medical Microbiology
Lecturer: Teaching Staff
At the end of the lecture you should be able to:
1. Discuss the treatment and prevention
of TB
2. Discuss
the
transmission,
pathogenesis,
clinical
features,
laboratory diagnosis, and treatment of
leprosy







Treatment of TB: Anti TB drugs, Duration of
therapy
Prevention: BCG vaccine,
Chemoprophylaxis
Leprosy: Description of the causative agent,
Epidemiology, Clinical findings (types of
leprosy: Lepromatous Leprosy - LL&
Tuberculoid Leprosy - TL).
Differences between LL and TL
Lab Diagnosis: Specimens, Microscopy,
(Culture is Not available), Lepromin skin
test, Animal inoculation
Antimicrobial chemotherapy of leprosy and
its duration
Prevention & Control of leprosy: Isolation of
LL patients, Chemoprophylaxis
(Insert here handouts and additional
pages for notes if needed)
Phase II
48
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Continue … Lecture 18: Mycobacteria (2)
Student Notes:


.
Multiple-drug therapy is used in the
treatment of TB for at least 6-9 months
Leprosy: LL & TL clinical features,
Treatment
Microbiology by Harvey, Champe and
Fisher , Second Edition (2007).
Publisher: Lippincott Williams &
Wilkins
In the computer cluster also you have the
opportunity to see some useful web sites about TB
and leprosy. We would recommend you look at the
following web sites:
http://www.cdc.gov
http://www.who.int
Self-assessment
Answer the following short question:
 Describe the causative agent of leprosy.
Discuss its pathogenesis, clinical findings,
laboratory diagnosis, treatment, and
prevention
Phase II
49
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Lectures 19- 21: Gram-negative Rods
Department: Medical Microbiology
Lecturer:
At the end of the lecture you should be able to:
1). Classify medically important Enteric Gramnegative rods (microaerophilic / aerobic) and Gramnegative anaerobes.
2). Describe the general characteristics of the family
enterobacteriaceae.
3). Discuss the antigenic structure of this group.
4). Discuss the epidemiology, virulence factors,
disease associations and treatment of the pathogenic
genera in this group.
5). Discuss the laboratory diagnosis of the common
pathogenic genera such as E.coli, Salmonella,
Shigella, Klebsiella and Proteus.
6). List members of this group which produce
opportunist infections.
7). Describe the epidemiology, virulence factors,
clinical diseases and laboratory diagnosis of
Pseudomonas aeruginosa.
8). Describe characteristics and importance of
microaerophilic members of group; Campylobacter
and Helicobacter.
9). Discuss the disease produced by Vibrio cholerae
Phase II
50
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
with emphasis on its prevention and diagnosis.
Most Gram-negative bacteria are aerobic or
facultative anaerobes and are motile with
peritrichous flagella. According to their effect on
lactose they are divided into two main groups which
are the lactose fermenters (also known as coliforms)
and the non-lactose fermenters. Their natural habitat
is the intestinal tract of humans or animals and they
may be commensals or pathogenic. Members of the
group have the O, K and H antigens. These are
virulence factors and are also used for laboratory
identification.
Some Enterobacteriaceae also
produce bacteriocins. Vibrio cholerae are the
causative agents of cholera. Epidemics are caused by
serogroups O1 and O139. Other serotypes usually do
not produce epidemics. Campylobacter and
Helicobacter are the microaerophilic curved Gramnegative rods. Campylobacter is often implicated in
diarrhoea whilst Helicobacter is known as a cause of
gastritis and ulcers. Pseudomonas aeruginosa is an
important opportunist bacteria. It is often implicated
in hospital acquired infections also.
Lactose fermenters can easily be distinguished
from non-lactose fermenters on MacConkey
agar. Other laboratory agar may be used for the
detection of Salmonella, Shigella and E.coli
specifically. The genus Salmonella has many
species S .typhi and S .paratyphi which cause
Enteric fever and S. enteritidis and S. typhimurim
which cause food poisoning. Diagnosis of
enteric fever can be made using blood or urine
samples in addition to faecal samples.
Antibodies may be detected in the patient’s
blood from the 7th to 10th day of illness.
Phase II
51
Medical Microbiology
Faculty of Medicine



King Abdul-Aziz University
Microbiology by Harvey, Champe and
Fisher. Second Edition (2007). Publisher:
Lippincott Williams & Wilkins
Murray. Medical Microbiology.
Mims. Medical Microbiology.
Self-assessment
Briefly answer the following Essay question:
1) Enumerate members of the group
Enterobacteriacae and mention one clinical
disease produced by each one. With regard to any
one member discuss the laboratory diagnosis and
treatment of any of them.
Phase II
52
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Lectures 22- 24: Parvobacteria
Department: Medical Microbiology
Lecturer:
At the end of the lecture you should be able to:
1). Describe the general characteristics of the
group.
2). Mention the six members of this group and
emphasise the genera which produce Zoonotic
infections.
3) Describe the specific characteristics used in the
identification of each genus.
4) Mention the epidemiology, virulence factors
and clinical infections produced by each member of
the group.
5) Discuss in detail the laboratory diagnosis for
Haemophilus, Bordetella and Brucella infections.
6) Discuss briefly laboratory diagnosis of
Legionella, Yersinia and Francisella.
7) Mention briefly infections produced by
Gardnerella vaginalis and Pasturella multicoida.
The term ‘Parvo’ means very small in size. All
members of this group are small Gram-negative
Phase II
53
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
cocco bacilli. The genera Haemophilus, Bordetella
and Legionella produce infections in humans only.
Whilst Brucella, Yersinea and Francisella produce
Zoonotic infections. Haemophilus influenze is
important in childhood infections whilst H.ducyrei
produces soft chancre and H.aegypti is known to
produce conjunctivitis. Bordetella pertusis is the
causative agent of whooping cough a severe
infection in children. The incidence of this disease
has declined greatly with the use of DPT vaccine.
Legionella pneumophilia is the causative agent of
Legionairres disease and Pontiac fever. The
organism is important in producing outbreaks of
atypical pneumonia. Brucellosis is an important
zoonotic disease often transmitted through milk and
dairy products. This disease should be considered in
cases of fever of unknown origin. Yersinia pestis (a
member of Enterobacteriacae)is best known for
bubonic plague or black death. Other manifestations
produced by this organism are pneumonic plague
and septacemia. Other members of this genus
Y.enterocolitica. Francisella tularensis is known
for producing tularaemia. Is regarded as a highly
dangerous organism. Human infections



Microbiology by Harvey, Champe and
Fisher. Second Edition (2007). Publisher:
Lippincott Williams & Wilkins
Murray. Medical Microbiology.
Mims. Medical Microbiology.
Self-assessment
Briefly answer the following Essay question:
1-Enumerate members of the group Parvobacteria
and diseases produced by each one. For any one
member of the group mention the laboratory
diagnosis and treatment.
Phase II
54
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Lecture 25: Spirochaetes (1)
Department: Medical Microbiology
Lecturer: Teaching Staff
Student Notes:
.
At the end of the lecture you should be able to:
1. Describe
the
morphology
of
Spirochaetes and their motility
2. Know all of the 3 genera of
Spirochaetes & their species and the
associated infections
3. Discuss
the
epidemiology,
transmission, clinical features &
stages,
laboratory
diagnosis,
treatment, and prevention of Syphilis
4. Also discuss the features of
congenital syphilis








Description of Spirochaetes
Motility by the axial filaments (periplasmic
flagellae)
Table of all genera & species of the
Spirochaetes and the associated infections
Syphilis:
Epidemiology,
Transmission
(sexual, transplacental, and blood for
transfusion)
Stages of Untreated Syphilis: Primary,
Secondary, Latent, and Tertiary Syphilis
Features of the Congenital Syphilis
Lab Diagnosis: Microscopy, Non-specific
Serological Tests, and Specific Serological
Tests. Culture is NOT available
Treatment, and Prevention
(Insert here handouts and additional
pages for notes if needed)
Phase II
55
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Continue … Lecture 25: Spirochaetes (1)
Student Notes:



.
Features of Spirochaetes
All 3 genera of the Spirochaetes & all of their
species and the associated infections
Syphilis
Microbiology by Harvey, Champe and
Fisher , Second Edition (2007).
Publisher: Lippincott Williams &
Wilkins
In the computer cluster also you have the
opportunity to see some useful web sites about
Syphilis. We would recommend you look at the
following web sites:
http://www.cdc.gov
http://www.who.int
Self-assessment
Answer the following short question:
 Discuss the clinical features, laboratory
diagnosis, and treatment of Syphilis.
Phase II
56
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Lecture 26: Spirochaetes (2)
Department: Medical Microbiology
Lecturer: Teaching Staff
Student Notes:
.
At the end of the lecture you should be able to:
1. Describe
the
epidemiology,
transmission,
clinical
features,
laboratory diagnosis, and treatment of
diseases caused by treponems other
than Treponema pallidum
2. Describe the causative agents, clinical
features, Lab diagnosis, and treatment
of Vincent's angina
3. Discuss
the
epidemiology,
transmission,
clinical
features,
laboratory diagnosis, and treatment of
diseases caused by Borrelia
4. Recognize the arthropod vectors of
Borrelia infections.
5. Discuss
the
epidemiology,
transmission,
clinical
features,
laboratory diagnosis, and treatment of
diseases caused by Leptospira






Bejel, Yaws, and Pinta: Causative agents,
Epidemiology, Transmission, Lab Diagnosis,
and Treatment
Vincent's Infection: the causative agents,
clinical features, Lab diagnosis, and
treatment
Relapsing Fever: Epidemic (louse-borne) RF,
Endemic (tick-born) RF, Epidemiology,
Clinical Features, Lab Diagnosis, and
Treatment
Lyme Disease: Epidemiology, Transmission,
Clinical Features, Lab Diagnosis, Treatment,
and Prevention
The arthropod vectors of Borrelia infections.
Weil's Disease: Transmission, Clinical
Features, Lab Diagnosis, Treatment, and
Prevention
(Insert here handouts and additional
pages for notes if needed)
Phase II
57
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Continue … Lecture 26: Spirochaetes (2)
Student Notes:
.
o Bejel, Yaws, and Pinta
o Vincent's Infection
o Relapsing Fever: Epidemic (louseborne) RF, Endemic (tick-born) RF,
o Lyme Disease
o Weil's Disease
Microbiology by Harvey, Champe and
Fisher , Second Edition (2007).
Publisher: Lippincott Williams &
Wilkins
In the computer cluster also you have the
opportunity to see some useful web sites about
Relapsing fever & Lyme Disease. We would
recommend you look at the following web sites:
http://www.cdc.gov
http://www.who.int
Self-assessment
Answer the following short question:
 Discuss the causative agents, clinical
features, laboratory diagnosis, and treatment
of Vincent's angina.
Phase II
58
Medical Microbiology
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Lecture 27: Chlamydia, Rickettsia, and Coxiella (1)
Student Notes:
.
Department: Medical Microbiology
Lecturer: Teaching Staff
At the end of the lecture you should be able to:
1. Differentiate between chlamydia and
viruses
2. Describe the morphology and the life
cycle of chlamydia
3. List all the species and serotypes of
Chlamydia and their associated
infections
4. Discuss
the
epidemiology,
transmission,
clinical
features,
laboratory diagnosis, treatment, and
prevention of diseases caused by
different serotypes of Chlamydia
trachomatis
5. Discuss the transmission, clinical
features, laboratory diagnosis, and
treatment of diseases caused by
Chlamydia pneumoniae






Differences between Chlamydia and Viruses
The life (reproductive) cycle of chlamydia
Differences between EB and RB
Table of all species & serortypes of the
Chlamydia and the associated infections
Epidemiology, Pathogenesis, Transmission,
Clinical Features, Lab Diagnosis, Treatment,
and Prevention of diseases caused by
Chlamydia trachomatis serotypes A to C, D
to K, and L1 to L3
Epidemiology, Pathogenesis, Transmission,
Clinical Features, Lab Diagnosis, and
Treatment of Atypical Pneumonia caused by
Chlamydia pneumoniae
(Insert here handouts and additional
pages for notes if needed)
Phase II
59
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Continue … Lecture 27: Chlamydia, Rickettsia, and Coxiella (1)
Student Notes:




.
Features of Chlamydia
The three species of the Chlamydia
Diseases caused by the different
serotypes of Chlamydia trachomatis
Atypical pneumonia caused by
Chlamydia pneumoniae
Microbiology by Harvey, Champe and
Fisher , Second Edition (2007).
Publisher: Lippincott Williams &
Wilkins
In the computer cluster also you have the
opportunity to see some useful web sites about
Chlamydia, Trachoma, and Atypical Pneumonia. We
would recommend you look at the following web
sites:
http://www.cdc.gov
http://www.who.int
Self-assessment
Answer the following short question:
 Discuss the clinical features, laboratory
diagnosis, and treatment of Chlamydial
Urethritis.
Phase II
60
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Lecture 28: Chlamydia, Rickettsia, and Coxiella (2)
Student Notes:
.
Department: Medical Microbiology
Lecturer: Teaching Staff
At the end of the lecture you should be able to:
1. Discuss
the
pathogenesis,
transmission,
clinical
features,
laboratory diagnosis, treatment, and
prevention of diseases caused by
Chlamydia psittaci
2. Differentiate between Rickettsia and
Viruses
3. Know the differences between
Rickettsia and Coxiella
4. Discuss the transmission, clinical
features, laboratory diagnosis, and
treatment of diseases caused by
Rickettsia
5. Discuss the transmission, clinical
features, laboratory diagnosis, and
treatment of diseases caused by
Coxiella burnetii





Epidemiology, Pathogenesis, Transmission,
Clinical Features, Lab Diagnosis, and
Treatment of diseases caused by Chlamydia
psittaci
Differences between Rickettsia and Viruses
Differences between Rickettsia and Coxiella
Endemic Typhus, Epidemic Typhus, and
Rocky
Mountain
Spotted
Fever:
Epidemiology, Pathogenesis, Transmission,
Clinical Features, Lab Diagnosis, Treatment,
and Prevention
Q Fever: Epidemiology, Pathogenesis,
Transmission,
Clinical
Features,
Complications, Lab Diagnosis, Treatment,
and Prevention
(Insert here handouts and additional
pages for notes if needed)
Phase II
61
Medical Microbiology
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Continue … Lecture 28: Chlamydia, Rickettsia, and Coxiella (2)
Student Notes:






.
Pneumonia caused by Chlamydia psittaci
Differences between Rickettsia and Viruses
Differences between Rickettsia and Coxiella
Typhus (Epidemic & Endemic)
Rocky Mountain Spotted Fever
Q Fever
Microbiology by Harvey, Champe and
Fisher , Second Edition (2007).
Publisher: Lippincott Williams &
Wilkins
In the computer cluster also you have the
opportunity to see some useful web sites about
Typhus, Spotted Fever, and Q Fever. We would
recommend you look at the following web sites:
http://www.cdc.gov
http://www.who.int
Self-assessment
Answer the following short question:

Discuss the epidemiology, clinical features,
laboratory diagnosis, treatment, and
prevention of Q Fever.
Phase II
62
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Lecture 29: Mycoplasma, Actinomyces & Nocardia
Department: Medical Microbiology
Lecturer: Teaching Staff
Student Notes:
At the end of the lecture you should be able to:
1. Recognize the basic morphologic
features of mycoplasma and
ureaplasma.
2. Discuss the involvement of these
bacteria in human disease.
3. List procedures used in the laboratory
diagnosis and agents used in the
treatment
4. Outline
the
similarities
and
differences between Actinomyces and
Nocardia.
5. List the most important species of
Actinomyces and Nocardia and the
types of infection with which they are
associated.
6. Discuss the laboratory diagnosis of
Actinomycoses and Nocardioses.
7. Describe the types of treatment
required for actimonycoses and
nocardioses.





The mycoplasmas are a group of small
bacteria with no peptidoglycan cell wall
Three species are associated with human
diseases: M. pneumoniae, M.hominis, and
Ureaplasma urealyticum
Associated disease(s) with each species
Lab Diagnosis and Treatment
Actinomyces and Nocardia: Most important
species (A. israeli and N. asteroids),
Diseases, Lab Diagnosis, and Treatment
(Insert here handouts and additional
pages for notes if needed)
Phase II
63
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Continue … Lecture 29: Mycoplasma, Actinomyces & Nocardia
Student Notes:



.
Atypical Pneumonia caused by M.
pneumoniae
STD caused by M.hominis, and Ureaplasma
urealyticum
Branching Bacilli: Actinomyces and
Nocardia
Microbiology by Harvey, Champe and
Fisher , Second Edition (2007).
Publisher: Lippincott Williams &
Wilkins
In the computer cluster also you have the
opportunity to see some useful web sites about
Mycoplasma, Actinomyces & Nocardia. We would
recommend you look at the following web sites:
http://www.cdc.gov
http://www.who.int
Self-assessment
Answer the following short question:
 Discuss the characteristics, clinical features,
laboratory diagnosis, treatment, and
prevention of diseases caused by
Mycoplasma.
Phase II
64
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Lectures 30-31: Mycology
Department: Medical Microbiology
Lecturer:
At the end of the lecture you should be able to:
1. Describe the characteristics of fungi.
2. Discuss differences between fungi and bacteria
with regard to size, cell structure and
reproduction.
3. Describe the different morphological types of
fungi (yeasts, moulds, dimorphic fungi and
deutromyces).
4. Mention sexual and asexual reproduction in
fungi. Brief outline of different types of spores.
5. Classify fungal infections according to the
different sites of the body involved.
6. Enumerate and describe superficial,
subcutaneous, cutaneous and systemic mycoses.
7. With regard to each of the above types of
infection describe transmission, clinical
symptoms, treatment and laboratory
diagnosis.
8. Outline opportunist fungal infections with
regard to epidemiology, pathogenesis,
symptoms, treatment and laboratory diagnosis.
9. Mention fungal toxins which produce
mycotoxicoses.
10. Summarise antifungal drugs and their mode of
action.
Phase II
65
Medical Microbiology
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Medical mycology is a study of fungi producing
disease in humans. Fungi are classified as
eukaryotic cells. Most fungi are either yeasts or
moulds. However, some fungi known as dimorphic
fungi can have both morphological types.
Superficial fungal infections involve the superficial
layers of the skin or hair. Mostly appear as areas of
hyper or hypo-pigmentation in the skin. Hair
infections may be on the scalp or in other parts of the
body. Dermatophytoses is a common manifestation
of fungal infections. May affect different parts of the
body and is produced by three different fungal
genera. Subcutaneous fungal diseases include
Chromoblastomycosis,
Sporotricosis
and
Mycetoma. Systemic fungal infections involve
several different fungi. They are all dimorphic fungi
and are transmitted often by inhalation producing
pulmonary infections which in many cases resemble
tuberculosis. Fungal agents which produce
opportunist infections differ in their nature and can
produce many different manifestations. There are
many pre-disposing factors for opportunist
infections but the most important group are the
immune-compromised. Some fungal agents produce
toxins which produce mycotoxicoses in humans the
best known example of this is aflatoxin. A limited
number of anti-fungal agents are available as they
have to be extremely selective in their toxicity since
fungi are eukaryotes as are their hosts.
The components of the fungal cell and the fungal
cell wall contains chitin while the cell membrane
has ergosterol. Conidiophores are the most
common type of asexual spore produced by fungi
and there is considerable variation in these with
regard to shape and size. The common name for
dermatophyte infections is “ringworm” or “tinea”.
These infections are named according to the site of
the body in which they occur. Systemic fungal
infections are more prevalent in some geographical
Phase II
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Medical Microbiology
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areas. In addition to pulmonary lesions produce
cutaneous lesions at the site of inoculation.

Microbiology by Harvey, Champe and
Fisher. Second Edition (2007). Publisher:
Lippincott Williams & Wilkins

Murray. Medical Microbiology.
Self-assessment
MCQ
1-Fungal cytoplasmic membrane contains:
A- Cholesterol.
B- Chitin.
C- Ergosterol.
D- Peptidoglycan.
Phase II
67
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Lectures 32-33: General virology
Student Notes:
.
Department: Medical Microbiology
Lecturer:
At the end of the lecture you should be able to:
1) Describe the basis structure of viruses,
viroids and prions
2) Distinguish between enveloped and nonenveloped viruses
3) List RNA and DNA viruses
4) Describe the symmetry of the virus
5) Define term of Atypical viruses
6) Describe the different method of Cultivation
of viruses
7) Name types of cell cultures and the
difference between them
8) How can detect and identify of growing virus
in cell cultures
9) Describe the different CPE of different
viruses on tissue culture
10) List the main steps of the virus multiplication
cycle
11) List the main steps of the viral pathogenesis
12) Define terms of chronic, latent , and slow
viral infections
13) Describe ways of virus entry, spread and exit
from the body
14) Name the different Antiviral Agents used and
mechanism of action of each one
15) Define interferon, their types
16) Describe the role of interferon in treatment of
viral infection and recession of some tumours
17) Recognize the difference between interferon
and immunoglobulin
(Insert here handouts and additional
pages for notes if needed)
Phase II
68
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
 Each virus particle or virion is composed of
capsid and a nucleic acid. Many viruses are
naked but some are enveloped. Some viruses have
enzymes.
 RNA Virus comprising 70% of all viruses. They
may be single-stranded or double-stranded. Also
may be either a sense strand, or an antisense
strand. All RNA viruses are single-stranded
except reovirus which is double-stranded. All
DNA viruses replicate in the nucleus except
poxviruses which replicate in the cytoplasm.
 All DNA viruses consist of double-stranded DNA
except for the parvoviruses, which have singlestranded DNA genome. All RNA viruses replicate
in the cytoplasm except retroviruses and influenza
viruses which replicate in the nucleus.
 Since viruses are obligate intracellular parasites,
they have to be grown in living cells as cell
cultures, embryonated eggs or laboratory animals.
Detection and identification of growing virus in
cell cultures: cytopathic effect, interference,
plaque formation, formation of inclusion bodies,
haemadsorption, fluorescent-antibody staining,
detection of viral antigen and neutralization tests.
 Viruses have no metabolic activity of their own.
Therefore, they depend on living cells for
providing energy and synthetic machinery for the
synthesis of: viral nucleic acid (genome) and
Viral proteins
 To produce disease, virus must enter a host, come
in contact with susceptible host, replicate, and
produce cell injury. Viruses may persist for a long
time in the host in one of the following forms:
Chronic infections, Latent infections or Slow
infections:

Antiviral Agents
1.
Drugs used for treatment of herpes viruses:
Acyclovir forscarnet, valacyclovir, famciclovir
and ganciclovir .
2.
Drugs used for treatment of Human
immunodeficiency (HIV): Nucleoside reverse
transcriptase
inhibitor:
Azidothymidine,
zidovudine, dideoxyinosine and dideoxycytidine,
Phase II
69
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
stavudine and lamivudine,
Non-nucleoside
reverse
transcriptase
inhibitor
(Nevirapine,Efavirenz ), HIV Protease Inhibitors:
(Saquinavir, Nelfrinavir, Amprenavir, Indinavir,
Lopinavir, Ritonavir ), Fusion inhibitors e.g.
Fuzeon (enfuvirtide), HAART regimen is a
combination of 2 nucleoside reverse transcriptase
inhibitors (AZT and ddI or 3TC or d4T) and a
protease inhibitor.
3.
Drugs used for treatment of other viruses:
Ribavirin is used in treatment of both DNA and
RNA viruses in infected cells, Amantidine and
rimantadine inhibit uncoating of influenza A but
not B.

Interferons are proteins that are members of
the large cytokine family. They are secreted by
most cells of vertebrates in response to viral
infections, or other selected stimuli. The antiviral
effects of IFNs are exerted through increased
expression of Class I and Class II MHC
glycoproteins,
antiproliferative
actions,
immunomodulatory effects and anti-viral activity
by direct inhibition of viral replication. IFNs
used in treatment of some viral disease,
treatment of tumour and improvement in
multiple sclerosis.
Phase II
70
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Continue … Lectures 32-33: General virology

Microbiology by Harvey, Champe and
Fisher. Second Edition (2007). Publisher:
Lippincott Williams & Wilkins

Murray. Medical Microbiology
Self-assessment
Briefly answer the following short question:



Enumerate the cytopathic Effect (CPE) of
growing virus in cell cultures?
The protein shell which encloses the viral
nucleic acid genome is
 Capsid
 Virion
 Envelope
 Nucleocapsid
Define the persistence of the virus,
enumerate its types and its mechanisms.
Phase II
71
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Lecture 34: Non-enveloped (Naked) DNA viruses
Student Notes:
.
Department: Medical Microbiology
Lecturer:
At the end of the lecture you should be able to:
1. Names Non-enveloped (Naked) DNA viruses
2. Unique features of each one
3. Describe the disease caused by adenoviruses,
papillomaviruses, and parvovirus B19
4. Describe the laboratory diagnosis of
adenoviruses
5. Describe the role of adenovirus in gene
therapy
6. Describe the disease mechanisms of
papillomaviruses
7. Recognize the importance of human
papillomaviruses in genital infections leading
to cervical carcinoma
Adenoviruses: Double-stranded linear, naked DNA.
It is the only virus has a fiber ( the organ of
attachment and haemagglutination. Adenoviruses
have been used in gene delivery for correction of
several humans’ diseases; including immune
deficiencies, cystic fibrosis, and even cancer.
 Diseases caused by adenoviruses: Acute
febrile pharyngitis and pneumonia,
Swimming pool conjunctivitis, conjunctivitis
and keratoconjunctivitis, Infantile
(Insert here handouts and additional
gastroenteritis and intussusceptions, Acute
pages for notes if needed)
haemorrhagic cystitis in children
 Detection of antibody titre is a good evidence
of infection by complement fixation and
Phase II
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72
Faculty of Medicine
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haemagglutintion inhibition. A living oral
attenuated vaccine was given to military
recruits
Papovavirus: Double-stranded circular naked DNA.
Consist of: Papillomaviruses and Polymaviruses.
 Diseases caused by papillomavirus:
Cutaneous warts, Mucosal warts: Anogenital
warts (Condylomata acuminate), Laryngeal
papillomas, Cervical dysplasia and neoplasia
(HPV types 16 and 18)
 Clinical manifestations of polyomaviruses:
Progressive multifocal leukoencephalopathy
(PML), Renal disease in
immunocompromized patients.
Parvovirus
 Single-stranded naked DNA
 Clinical presentations of B19: Erythema
infectiosum (Fifth disease or Slapped-Cheek
syndrome), A plastic crisis, hydrops fetalis
Self-assessment
MCQ
Adenoviruses:
A. Are RNA-containing viruses
B. Are human oncogenic viruses
C. Are limited in their distribution
D. Firstly discovered in the human adenoid
tissues
Phase II
73
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Lectures 35: Enveloped DNA viruses (Poxviridae)
Department: Medical Microbiology
Lecturer:
At the end of the lecture you should be able to:
1) Describe the important properties of
poxviruses
2) Appreciate the effect for the eradication of
small pox and the basis for this
accomplishment
3) Describe the disease mechanisms of poxvirus
4) Causes of successful eradication of small pox
5) Appreciate that some poxviruses can be
transmitted to man as zoonotic infections and
that there is still real danger of their spread
Poxviruses are the largest oval to brick-shaped
viruses.
 Double- stranded DNA, replicate in the
cytoplasm, has Guarnieri's bodies.
 Characters of smallpox rash: Monomorphic,
centrifugal, leaving scarred area
 Death results from overwhelming toxaemia
and systemic shock
 Isolation of the virus using chick embryo or
tissue culture.
 Direct detection of virus by electron
microscopy, of viral antigens by
immunofluorescence, of virus gene by PCR.
 In 1967s the WHO embarked on a vaccination
campaign contains live, attenuated vaccinia
virus that led the eradication of smallpox. The
last naturally occurring case was in Somalia in
1977.
 Its possible use as a biological weapon
Phase II
74
Medical Microbiology
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King Abdul-Aziz University
Molluscum contagiosum virus causes warts of the
skin and mucous membrane usually in a cluster. The
lesions are self-limited
Orthopoxvirus includes variola virus, vaccinia
virus, monkey pox virus, and cowpox virus. Their
symptoms are similar to smallpox but differ in
occurrence of lymphadenopathy, lower mortality and
transmissibility.
Parapoxvirus causes orf virus infections
Self-assessment
MCQ:

A.
B.
C.
D.
The largest and most complex viruses are
Arboviruses
Picornaviruses
Poxviruses
Herpes viruses
Phase II
75
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Lecture 36: Enveloped DNA viruses (Herpesviridae) (1)
Department: Medical Microbiology
Lecturer:
At the end of the lecture you should be able to:
1) Describe the important properties of the
family of herpesviruses
2) List the members of this family
3) Describe the tendency of these viruses to
cause latent infections
4) Site of latency of each virus
5) Role of some herpesviruses in occurrence of
human cancer
6) Describe the difference between HSV1
&HSV2 as regard; their mode of
transmission, their clinical manifestation,
their sit of latency, their reactivation and
their prevention
7) Appreciate the value of virus culture in the
diagnosis of herpes simplex viruses
8) Appreciate the effectiveness of antiviral
therapy in herpes viruses diseases
Herpesviruses: Enveloped double stranded linear
DNA, have glycoprotein spikes.
 Establish latent infections, persist
indefinitely in infected hosts. Frequently
reactivated in immunosuppressed host
 Some are cancer-causing.
Herpes simplex viruses (HSV) type 1 &type 2
 HSV-1 spreads by contact. Its lesions are
above the waist
 Primary infections of HSV type 1:
Gingivostomatitis; Pharyngitis or tonsillitis
Keratoconjunctivitis, Encephalitis,
Disseminated infections, such as pneumonia
in immunosuppressed patients, Herpetic
whitlow
Phase II
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Medical Microbiology
Faculty of Medicine






King Abdul-Aziz University
Latent infections: In the trigeminal ganglia.
Its reactivation as herpes labialis and heal
without scaring
HSV-2 is transmitted sexually or to
newborns during birth. Its lesions are below
the waist.
Primary infections of HSV type 2:Genital
herpes, Neonatal herpes including meningitis
or encephalitis.
Latent infections: In the sacral or lumber
ganglia
The presence of multinucleated giant cells
suggests HSV infection
Acyclovir is used for all herpetic infections.
Foscarnet is used for acyclovir resistant cases
Self-assessment

Describe the important properties of
herpes viruses; enumerate its classification
showing the site of latency and the diseases
produced by each of them?

MCQ: The most common recurrent
disease produced by herpes virus type 1 is:
Acute herpetic gingivostomatitis
Herpes labialis
Keratoconjunctivitis
Encephalitis
A.
B.
C.
D.
Phase II
77
Medical Microbiology
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King Abdul-Aziz University
Lecture 37: Enveloped DNA viruses (Herpesviridae) (2)
Student Notes:
.
Department: Medical Microbiology
Lecturer:
At the end of the lecture you should be able to:
1) Describe the major clinical manifestation of
infection by varicella-zoster virus
2) Describe two distinct diseases caused by
varicella-zoster virus
3) Difference between small pox and
chickenpox rash
4) Realize the availability of the varicella zoster
vaccine and its routine use for all children
5) Describe the mode of transmission of CMV
6) Describe the effect of congenital infection by
CMV
7) Describe features of transmission and acute
infection(infectious mononucleosis) by EBV
8) Role of some herpesviruses in occurrence of
cancer
(Insert here handouts and additional
pages for notes if needed)
Phase II
78
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Continue … Lecture 37: Enveloped DNA viruses (Heresviridae) (2)
Student Notes:

Microbiology by Harvey, Champe and
Fisher. Second Edition (2007). Publisher:
Lippincott Williams & Wilkins

Murray. Medical Microbiology
.
Self-assessment
MCQ

All of the following statements concerning
varicella and zoster are correct EXCEPT:
A. Both are caused by the same virus
B. Zoster is a primary contact with
the virus
C. Varicella a primary contact with
the virus
D. Varicella is a highly infectious
disease of children
Phase II
79
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Lecture 38: Hepatitis viruses
Student Notes:
.
Department: Medical Microbiology
Lecturer:
At the end of the lecture you should be able to:
1) List viruses that primarily infect the liver
(hepatitis viruses)
2) Describe the differences between these
viruses as regard type of virus, mode of
transmission, prevalence, fulmination,
chronicity, Oncogenicity
3) Describe the different methods of prevention
and control of these viruses
4) Describe the role of HBV and HCV in liver
cirrhosis and HCC
5) Identifies the main serological markers used
in the diagnosis of types of viral hepatitis
6) Describe the importance of blood screening
for the prevention of transfusion-associated
hepatitis and the types of tests routinely
performed in the blood bank
7) Appreciate the importance of water and food
hygiene in the prevention of HAV and HEV

Characteristics of hepatic viruses
(Insert here handouts and additional
pages for notes if needed)
Phase II
80
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Continue … Lecture 38: Hepatitis viruses
Student Notes:

Microbiology by Harvey, Champe and
Fisher. Second Edition (2007). Publisher:
Lippincott Williams & Wilkins

Murray. Medical Microbiology
.
Self-assessment
MCQ

In hepatitis B infected patients, the most
important indicator of active virus
replication and risk of transmissibility is
A. HBsAg
B. HBeAg
C. HBcAg
D. HBsAb
Phase II
81
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Lecture 39: Non-enveloped (Naked) RNA viruses
Student Notes:
.
Department: Medical Microbiology
Lecturer:
At the end of the lecture you should be able to:
1) List Non-enveloped (Naked) RNA viruses
2) Recognize the important properties of
picornaviruses
3) Describe Clinical types of poliomyelitis
4) Discuss the advantages and disadvantages of
Salk and Sabin
Picornaviruses: Positive sense single-stranded nonenveloped RNA viruses




There are three antigenic types of
polioviruses. Polioviruses have a tropism for
the epithelial cells lining the alimentary tract
and for cells of the central nervous system.
Clinical types of poliomyelitis : Inapparent
infection, abortive infection, aseptic
meningitis and paralytic poliomyelitis
Poliomyelitis is diagnosed by isolation of the
virus from stools or throat on tissue culture,
detection of antibodies by neutralization or
complement fixation tests or PCR to detect
viral RNA in blood.
There are Two vaccines (Salk and Sabin)
contain the three types of virus, produce
neutralizing antibodies, and prevent CNS
infection.
(Insert here handouts and additional
pages for notes if needed)
Phase II
82
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Continue … Lecture 39: Non-enveloped (Naked) RNA viruses
Student Notes:

Microbiology by Harvey, Champe and
Fisher. Second Edition (2007). Publisher:
Lippincott Williams & Wilkins

Murray. Medical Microbiology
.
Self-assessment

Describe the important properties of
poliovirus, its pathogenesis and how can
be prevented?
Phase II
83
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Lecture 40: Non-enveloped (Naked) RNA viruses
Student Notes:
.
Department: Medical Microbiology
Lecturer:
At the end of the lecture you should be able to:
1) Describe the different syndromes of
coxsackievirus infections
2) List the other enteroviruses and the disease
caused by each one
3) Describe the clinical manifestations of
rhinoviruses
4) List the viruses that cause gastroenteritis
5) Recognize the importance of hygiene and
oral rehydration therapy in the control of
viral gastroenteritis

Syndromes of Coxsackievirus infections:
A. Group A- specific diseases: Herpangina,
Hand-foot and mouth disease and Acute
hemorrhagic conjunctivitis
B. Group B- specific diseases: Pleurodynia,
Pericarditis, Neonatal myocarditis and
Insulin-dependent diabetes in young children
C. Diseases caused by both groups: Aseptic
meningitis, Minor respiratory illness and
upper respiratory tract infections
D. Enteroviruses 68 cause pneumonia in
children,
Enteroviruses
70
cause
haemorrhagic conjunctivitis, Enteroviruses
71 cause meningitis or encephalitis.
Rhinoviruses are the main cause of common cold.
No specific antiviral therapy is
(Insert here handouts and additional
pages for notes if needed)
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Student Notes:
.

and development of an effective vaccine are
difficult because of multiple rhinovirus
serotypes, poor humoral antibody response
and the secretory antibody (IgA) that is vital
in conferring protection is not long lasting.
 Rotaviruses; Non-enveloped, double capsid;
ether and acid stability. The genome of 10
segments of double-stranded RNA. Rotavirus
is the most common cause of gastroenteritis
in young children. Diagnosis by detection of
the virus in the stool by RIA or ELISA,
detection of antigen by ELISA or detection
of 4-fold rise in antibody titre. There is
neither antiviral therapy nor a vaccine
available.
Caliciviruses Non-enveloped positive-single
stranded RNA, non-segmented genome. Norwalk
virus is the human Calicivirus. It causes epidemic
acute gastroenteritis especially in children.
Radioimmunoassay and ELISA tests are used to
detect the presence of antibodies or PCR for
detection of the genome. No specific antiviral
treatment
Self-assessment
MCQ

Which of the following statements is true
regarding rhinoviruses?
A. There are ten known serotypes
B. They induce long-life immunity
C. They are transmitted from person
to person through close contact √
D. They are isolated from faeces
(Insert here handouts and additional
pages for notes if needed)
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Lecture 41: Enveloped RNA viruses (Orthomyxoviruses)
Student Notes:
.
Department: Medical Microbiology
Lecturer:
At the end of the lecture you should be able to:
1) Describe the important properties of
orthomyxoviruses (influenza virus)
2) Recognize the types and subtypes of
influenza virus and their role of medical
importance
3) Distinguish between the mechanisms of
antigenic drifts and antigenic shifts
4) Describe the complications of influenza virus
infections
5) Recognize the presence and limitation of the
influenza vaccines
6) Recognize the possibility of use of antiviral
agents in influenza
7) Describe the transmission and important of
avian influenza virus
 Influenza viruses spherical, single stranded,
negative sense segmented enveloped RNA with
spikes (haemagglutinin and neuraminidase). The
only RNA viruses that replicate in the nucleus.
Genetic reassortment is common
 Antigenic variation:
1) Antigenic drifts: It is minor changes due to
mutation in the viral RNA.
2) Antigenic shifts: It is major changes due to
reassortment of gene segments.
 Influenza may be complicated by bacterial
pneumonia or Reye's syndrome
 There are two types of vaccines used for
prevention of influenza
(Insert here handouts and additional
1) A killed vaccine containing purified protein
subunits of the virus (HA and NA) for both type pages for notes if needed)
A and B influenza virus.
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2) A living attenuated cold adapted vaccine
containing temperature-sensitive mutants of
influenza A and B.
 A new avian influenza strain (H5N1) jumping
directly from the avian host to humans. Close
contact with infected poultry has been the primary
source for human infection. No reports of humanto-human transmission of the virus. Genetic studies
confirm that the influenza A virus H5N1 mutates
rapidly
allowing
easy
human-to-human
transmission, a pandemic could ensue. At this
time, H5N1 virus will lead to a global disease
outbreak in humans.
Self-assessment


A.
B.
C.
D.
Describe the important properties of
influenza virus, distinguish between its
antigenic shifts and drift and how can be
prevented?
MCQ:
Which of the following statements is true
concerning antigenic shift of human influenza
virus?
It is a major changes, resulting in appearance of
a new subtype √
It is exhibited by influenza B and C viruses
It is due to mutation in the gene
It does not affect the viral surface protein
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Lecture 42: Enveloped RNA viruses (Paramyxoviruses)
Student Notes:
.
Department: Medical Microbiology
Lecturer:
At the end of the lecture you should be able to:
1) Describe the difference in the structure and
genome between orthomyxoviruses and
paramyxoviruses
2) Recognize the importance of parainfluenza and
RSV in infants and childhood disease
3) Identify some of the major features of mumps
4) Report some complications caused by mumps
including orchitis
5) Identify some of the major features of
measles including koplik's spots and
distribution of its rash
6) Recognize the complications caused by measles
including pneumonia and SSPE
7) Describe the important properties of togaviruses
8) Recognize the danger of congenital rubella
syndrome
9) Describe the importance of serologic testing
(anti-rubella IgM and IgG) in recent
diagnosis and assessment of the immunity of
rubella
10) Report the effectiveness and value of MMR
vaccine in controlling of measles, mumps
and rubella
11) Describe the important properties of
coronaviruses
12) Identify the severe acute respiratory
syndrome (SARS)
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 Paramyxoviruses Spherical, single stranded
enveloped RNA, linear, non-segmented, negativesense with spikes that contain haemagglutinin and
neuraminidase (HN; attachment protein), or fusion
proteins (F; fusion to susceptible host).
Antigenically stable. Parainfluenza and
Respiratory syncytial viruses cause localized
infections; while measles and mumpus viruses
cause systemic infections.
 Parainfluenza virus is a major cause of
respiratory disease in infants and young adults.
 Respiratory syncytial virus (RSV) is the most
important cause of bronchiolitis and pneumonia in
infants.
 Mumps is an acute contagious disease
characterized by non-suppurative enlargement of
the parotid glands. It may be complicated by
orchitis that lead to sterility.
 Measles is a highly infectious disease that affects
children that is characterized by fever and
maculopapular skin rash. It may be complicated by
Pneumonia, Otitis media, Encephalitis or Subacute
sclerosing panencephalitis
 Rubella (acute infectious disease characterized by
fever, rash and enlargement of occipital and
cervical lymph nodes) & congenital rubella
syndrome are caused by Togavirus. Detection of a
rising titre of rubella IgG or detection of rubella
IgM antibodies in pregnant women is diagnostic of
recent rubella infection. Also detection of rubella
IgM antibodies in the newborn is diagnostic of
infection in utero.
 MMR is an effective vaccine for mumps, measles
and rubella is given to children at the age of 15
months. Another dose is recommended before
school entry
 Coronaviruses cause colds and severe acute
respiratory syndrome (SARS)
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Continue … Lecture 42: Enveloped RNA viruses (Paramyxoviruses)
Student Notes:

Microbiology by Harvey, Champe and
Fisher. Second Edition (2007). Publisher:
Lippincott Williams & Wilkins

Murray. Medical Microbiology
.
Self-assessment

Describe the important properties of
measles virus, pathogenesis of its infection
and its complications?

MCQ: What is the most dominant method
of spread for measles?
A. Faeco-oral rout
B. Fomite spread
C. Respiratory droplet spread
D. Sexual contact
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Lecture 43: Rhabdoviruses – Slow Viruses - Prions
Student Notes:
.
Department: Medical Microbiology
Lecturer:
At the end of the lecture you should be able to:
1) Describe the Important properties of
Rhabdoviruses
2) Appreciate the lethality of rabies virus
infection and that it is one of the main
zoonotic infections in man
3) Name the type of inclusion bodies caused by
rabies virus and their utilization in the
diagnosis of rabies
4) Identify serologic tests used of detection
rabies virus infection
5) Appreciate the history of development of the
rabies vaccine and the circumstances for its
use in man and domestic animals
6) Notes about haemorrhagic fever viruses
7) Identify slow infection diseases that are
caused by conventional viruses and
unconventional agents i.e. prions.
8) Describe the nature of prions and characters
of prions- mediated diseases
9) List some prion diseases and recognize the
possibility of iatrogenic transmission of
prions
Rhabdoviruses
 Bullet-shaped, enveloped -ve SS RNA
producing "Negri bodies"; characteristic for
rabies virus. Rabies virus has a broad host
range
 Rabies results from the bite of the rabid
(Insert here handouts and additional
animal by saliva.
 It multiplies locally in the muscles then pages for notes if needed)
travels via the peripheral nerves to the CNS
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where it multiplies causing fatal encephalitis.
Rabies virus infection is diagnosed by
detection
of
the
antigens
by
immunofluorescence, or by isolation of the
virus by intracerebral inoculation of mice, or
by RT-PCR or by detection of the antibodies
by
immunofluorescence,
ELISA
or
neutralization tests.
All vaccines for human use contain
inactivated rabies virus(Human diploid cell
vaccine, Rabies vaccine adsorbed, Purified
chick embryo cell vaccines )
Slow diseases
 Slow diseases caused by conventional
viruses: progressive multifocal
leukoencephalopathy is caused by JC viruses,
saubacute sclerosing panencephalitis is
caused by measles virus and HIV or by
unconventional agents or prions
 Prions are infectious particles composed of
proteins with no detectable nucleic acid.
They cause degeneration and spongiform
changes in the CNS with long incubation
period and there is no inflammation or
immune response to these diseases as they
are normal human proteins.
 They are transmitted by ingestion of infected
tissues mainly the brain, or from
contaminated surgical instruments.
 Prions diseases are Kuru, Creutzfeldt-Jakob
disease and Variant Creutzfeldt-Jakob
disease
Self-assessment

MCQ: When Rabies is present in a
community, any dog that has bitten a
person must be quarantined for how long?
A. At least 3 dyes
B. At least 5 dyes
C. At least 10dyes
D. Confinement is not really
necessary
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Lecture 44: Arboviruses
Student Notes:
.
Department: Medical Microbiology
Lecturer:
At the end of the lecture you should be able to:
1) Define the term arboviruses
2) Recognize the role of insects as vectors and
animals as reservoirs of arbovirus infections
3) List the names of the major families of
viruses causing encephalitis
4) Appreciate the impact of major arbovirus
diseases on man
5) List major arbovirus diseases in Saudi Arabia
and the surrounding countries and how to
prevent
Arbovirus
 The term Arbovirus is an acronym for
arthropod-born virus that these viruses are
transmitted
by arthropods,
primarily
mosquitoes and ticks. It is classified into 3
families; togaviridae (Envelope singlestranded, positive RNA), flaviviridae
(Enveloped single-stranded, positive RNA)
and bunyaviridae (Enveloped three segments
of negative- sense RNA).
 Diseases caused by Arboviruses present in
one of the following pictures: encephalitis,
haemorrhagic fever, fever rash and
lymphadenopathy
 Different encephalitis arboviruses in the
Togavirus and Flavivirus groups are endemic
in many parts of the world.
Yellow fever: There are two distinct cycles (Jungle
and Urban) exist in nature, with different reservoirs
and vectors: It can diagnosed by Isolation of the
virus from the blood or detection of neutralizing
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antibodies or complement-fixation antibodies. It is a
preventable diseases by17-D vaccine
Dengue fever (Breakbone fever): There are two
types of dengue fever: Classic and Haemorragic that
is called dengue fever shock. (Mortality rate 10%).
 Serological diagnosis to detect the presence
of
neutralizing
antibodies,
haemagglutination-inhibiting antibodies or
complement-fixation antibodies.
 No antiviral therapy or vaccines for dengue
 Some important diseases caused by
bunyavirus Sand fly FeverRift Valley Fever
Hantaviruses
Self-assessment
Briefly answer the following short question:



What are prions. Describe the human diseases
caused by them?
Describe the epidemiologic cycles of yellow
fever and how can be prevented?
MCQ: Which one of the following statements
concerning yellow fever is correct?
A. Monkeys in the Jungle are a
major reservoir
B. Ribavirin is specific therapy
C. The causative agent is DNA
double-stranded virus
D. The disease is transmitted
sexually
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Lecture 45: Retroviruses - Oncogenesis
Student Notes:
.
Department: Medical Microbiology
Lecturer:
At the end of the lecture you should be able to:
1) Relate the role played by HTLV in human
diseases and the presence of screening tests
for the prevention of their transmission by
blood transfusion
2) Describe the Important properties of HIV
genome, including the role of reverse
transcriptase
3) Describe the steps of reterovirus
multiplication, including its integration in the
host cell DNA
4) Describe the Mode of transmission of HIV
5) Describe the clinical manifestations of HIV
infection, including its relation with
immunological cells
6) Identify serologic tests used of detection of
HIV infection
7) Appreciate and practice universal precautions
to prevent exposure to blood in the
laboratory



Retroviruses
Two identical single stranded positive-sense
enveloped RNA tightly complexed with p7
and the enzymes; reverse transcriptase,
integrase and a protease. Non-oncogenic and
cytocidal. Infect cells of immune system;
helper (CD4) T lymphocytes, resulting in the
loss of CMI and a high probability of
opportunistic infections
Transmitted Sexually, parenterally, from
mother to foetus
HIV attacks CD4 helper T cells leading to
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their depletion with increasing
in the
frequency of opportunistic infections.
HIV is diagnosed by decreased CD4 cells
count, detection of HIV antibodies, detection
of viral nucleic acid by PCR, detection of
viral antigens and Virus isolation from
lymphocytes, bone marrow or plasma.
Vaccine production to HIV is difficult due to
rapid mutation of the virus and absence of an
appropriate animal model.
Self-assessment

Describe the genome of HIV, its genes,
important mode of its transmission, three
stages of its clinical findings and how can
be prevented?

MCQ: The gp120 of HIV
A. Binds to the host CD4 cells
B. Binds to the host CD8 cells
C. Is an internal protein
D. Is not responsible for the antigenicity
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Practical 1:
Sterilisation and Disinfection
TUTOR:
Department: Medical Microbiology
SUMMARY:
Sterilisation means the complete removal or destruction of all forms of all living organisms;
this includes bacterial endospores. The methods of sterilisation are: Filtration, Dry heat
(flaming, incineration), Moist heat (boiling, pasteurisation, steaming, pressure steaming),
Radiation (gamma-rays, ultraviolet rays), Chemicals (phenol, ethyl alcohol, formalin).
OBJECTIVES:
At the end of the practical you should be able to:
1) Describe and discuss the main methods of sterilisation, disinfection, antiseptics and aseptic
technique.
2) The application of different types of sterilisation in hospitals and clinical laboratories.
3) Physical methods of sterilisation include heat, radiation, filtration and sterilisation by gas.
4) Chemical methods of sterilisation involve use of disinfectants.
5) Indicators must be included in all methods used in order to assure strict quality control.
Sterilisation is the killing of all living forms of microbes or their exclusion from an object.
Heat is the most efficient method of sterilisation for objects which can withstand high
temperatures. Dry heat may be used as red heat or in hot air ovens. Efficiency of hot air
oven is monitored by Bacillus subtilis spores. Moist heat methods are more efficient and
autoclaving is considered to be the most efficient method of sterilisation. Irradiation
methods include the use of gamma rays and X-rays. Such methods can be used for
sterilisation of items such as surgical packs, syringes, catheters and syringes. Filtration
techniques are best for heat labile compounds such as antibiotic solutions, hormones or
vitamins. Sterilisation by gas is useful for heat sensitive medical devices such as prosthetic
heart valves or catheters.
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Disinfection differs from sterilisation because it destroys the vegetative bacteria but does
not destroy the spores. Disinfection may be carried out by moist heat, ultraviolet radiation
and by chemicals. Ideal disinfectants and antiseptics must have certain properties.


Mackie and McCartney. Practical Medical Microbiology.
Microbiology by Harvey, Champe and Fisher. Second Edition (2007). Publisher:
Lippincott Williams & Wilkins
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Practical 2:
Microscopy – Bacterial Growth and Metabolism
TUTOR:
Department: Medical Microbiology
SUMMARY:
Microscopy can provide important information for rapid presumptive diagnosis. Gram- stain
is commonly used in laboratories and helps to identify the pathogen by indicating whether it
is Gram-positive or Gram-negative and also whether it is a coccus or a bacillus.
OBJECTIVES:
At the end of the practical you should be able to:

Prepare and fix smears prior to staining.

Indicate precautions required when using staining techniques.

Use the Gram staining technique independently.

Discuss the principle of the Ziehl-Neelsen stain.

Discuss the use of the wet preparation.
Gram staining reaction is used to help identify pathogens in specimens and cultures by their
Gram reaction and morphology. Gram-positive bacteria stain dark purple and are not
decolorised by acetone or ethanol. Examples include species of: Staphylococcus,
Streptococcus, Clostridium, Bacillus and Corynebacterium. Gram negative bacteria stain
red. They are decolorised by acetone or ethanol and take up the red counter stain. Examples
include species of: Neisseria, Haemophilus, Enterobacteria, Vibrio, Brucella and Yersinia.


Microbiology by Harvey, Champe and Fisher. Second Edition (2007). Publisher:
Lippincott Williams & Wilkins
Mackie and McCartney. Practical Medical Microbiology.
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Practical 3:
Laboratory Media, Culture (Isolation) & Sensitivity Testing
TUTOR:
Department: Medical Microbiology
SUMMARY:
Bacteria have certain requirements in order to grow. These include;
 Optimal physical conditions (gaseous requirement, temperature, pH and water).
 Suitable nutrients in the form of media (liquid, solid or biphasic).
 Many different types of media are available for use in microbiology laboratories.
The purpose of using cultural techniques in microbiology is to demonstrate the presence of
organisms which may be causing disease and when indicated to test the sensitivity of
pathogens to antimicrobial agents.
OBJECTIVES:
At the end of this practical students will be expected to know:

Bacteriology laboratory use media of different types these are mainly Basic media,
Enriched media Selective media and Differential media. Some media can be both
differential and selective in their properties.

Examples of common media such as Blood agar, Chocolate agar and MacConkey agar
should be easily recognised and students should be familiar with media in all categories.

Some media have special uses such as for transport of specimens, anti-microbial
sensitivity tests or culture of anaerobic organisms.



Be familiar with the technique used to inoculate media in Petri dishes which can provide
single colonies for identification.
Practically perform the ‘plating’ out or ‘looping’ technique used most commonly in
microbiology in order to obtain single colonies.
Know the importance of obtaining pure cultures as most clinical specimens give rise to
mixed cultures.
Basic media such as nutrient agar can be enriched using blood or serum to produce enriched
media which may be used for more fastidious organisms. Selective media contain substances
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that inhibit all but a few types of bacteria and facilitate the isolation of a particular species
from a mixed inoculum. Differential media reveal specific characteristics of certain groups
of bacteria. Such media contain indicators which change visibly with the growth of bacteria.
Combinations of selective and differential media may be used in selection of pathogens and
their differentiation using specific characteristics.
Petri dishes with agar are dried in an incubator for 15-20 min before use. Sterile
bacteriological loops are used to apply the inoculum. The loop is sterilised again and the
inoculum is spread in two or three quadrants. Inoculated media is incubated at 37 C for 24 h.
The method for inoculating agar slopes differs by streaking the centre of the slope and the
inoculum is then spread in a zigzag pattern.

Microbiology by Harvey, Champe and Fisher. Second Edition (2007). Publisher:
Lippincott Williams & Wilkins

Mackie and McCartney. Practical Medical Microbiology.
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Practical 4:
Staphylococci – Streptococci – Enterococci
TUTOR:
Department: Medical Microbiology
SUMMARY:
The three main staphylococcal species are:
1. Staphylococcus aureus
2. Staphylococcus epidermidis
3. Staphylococcus saprophyticus
The Streptococci are divided into beta- and alpha-haemolytic streptococci
The enterococci also appear as Gram-positive cocci arranged in short chains. They result into
blackening of aesculin agar plate
OBJECTIVES:
At the end of the practical students will be expected to:





Be familiar with the basic laboratory tests used to identify Staphylococcus aureus
including:
o Gram smear : Gram-positive cocci arranged in clusters
o Colonial morphology : yellow or golden colonies
o Catalase-positive
o Coagulase-positive
o DNAase-positive
o Mannitol-fermenter
Recognise that MRSA (methecillin-resistant Staphylococcus aureus) are resistant to
oxacillin and usually sensitive to vancomycin
Know that novobiocin differentiates between Staphylococcus epidermidis (sensitive) and
Staphylococcus saprophyticus (resistant)
Be able to recognise beta- and alpha-haemolysis
Be familiar with the basic laboratory methods used to grow and identify:
o Streptococcus pyogenes
o Streptococcus pneumoniae
o Enterococcus

All staphylococci are Gram-positive cocci arranged in clusters & Catalase-positive

Staphylococcus aureus is Coagulase-positive and DNAase-positive, Yellow colonies,
Mannitol-fermenter
Oxacillin (Flucloxacillin) is the usual antibiotic used against staphylococcal infections

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
Vancomycin is used to treat infections caused by MRSA

Staphylococcus epidermidis is sensitive to novobiocin while Staphylococcus
saprophyticus is resistant

All streptococci and enterococci are catalase-negative

Streptococcus pyogenes :
o Gram-positive cocci arranged in long chains
o Beta-hemolytic on blood agar plate (BAP)
o Bacitraci-sensitive
o Lancefield grouping: Group A

Streptococcu pneumoniae:
o Gram-positive cocci arranged in pairs (diplococci). Some are in short chains
o Alpha-haemolytic on BAP
o Colonies: disc-shaped with raised edges (draughtsman)
o Optochin-sensitive

Enterococcus
o Gram-positive cocci arranged in short chains
o Results in blackening when grown on bile aesculin agar


Microbiology by Harvey, Champe and Fisher , Second Edition (2007). Publisher:
Lippincott Williams & Wilkins
Mackie and McCartney. Practical Medical Microbiology.
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Practicals 5 & 6:
Neisseria & Gram-positive Rods
TUTOR:
Department: Medical Microbiology
SUMMARY:
o Nisseriae are Gram-negative diplococci. They grow on chocolate agar plate in 5-7%
carbon dioxide atmosphere. They are Oxidase-positive
o GPRs are divided into Spore-formers & Non Spore-formers
OBJECTIVES:
At the end of the practical students will be expected to:


Be familiar with the basic laboratory methods used to grow and identify:
o Neisseria meningitides
o Neisseria gonorrheae
Be familiar with some basic laboratory methods used to grow and identify GPRs eg:
o Recognise Clostridium tetani terminal spores (Microscopy: drumstick
appearance)
o Recognise Robertson's cooked meat medium
o Recognise the anaerobic jar
o Recognise the tellurite plate & Loeffler's serum slope medium used to grow
Corynebacterium diphtheriae
o Gram & methylene blue stained smears of Corynebacterium diphtheriae

Neisseriae are:
o Gram-negative diplococci
o They require 5-7% carbon dioxide for growth on chocolate agar plate.
o Thayer-Martin agar is a selective media (contains antimicrobials)
o Oxidase-positive

Carbohydrates Utilisation Tests : N. meningitidis : utiles maltose & glucoseN.
gonorrheae: utilises glucose only

GPRs :
o Spore-formers are: Bacillus & Clostridium (anaerobic)
o Non spore-formers are: Corynebacterium & Listeria
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
Microbiology by Harvey, Champe and Fisher, Second Edition (2007). Publisher:
Lippincott Williams & Wilkins

Mackie and McCartney. Practical Medical Microbiology.
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Practical 7 & 8:
Mycobacteria, Gram-negative Rods & Parvobacteria
TUTOR:
Department: Medical Microbiology
SUMMARY:
o Mycobacteria are acid-fast bacilli (AFB)
o Mycobacterium tuberculosis can be grown on special media e.g. Lowenstein-Jensen
Medium
o GNRs: This group includes the enteric Gram-negative bacteria which are aerobic or
facultative anaerobes. According to their effect on lactose they are divided into:
Lactose fermenters and non-lactose fermenters.
o The term ‘Parvo’ means very small in size. All members of the group are small Gramnegative cocco-bacilli. They vary in their normal habitat and the clinical infections
that they produce. This laboratory session will mainly deal with the laboratory
diagnosis of Haemophilus species.
OBJECTIVES:
At the end of the practical students will be expected to:
o Recognise AFB
o Recognise Lowenstein-Jensen Medium
At the end of the GNR session the student should be able to identify:

E. coli as a common example of a lactose fermenter with its cultural and microscopic
characteristics.

K. pneumoniae as another important member of this group which is also a lactose
fermenter.

Proteus as non-lactose fermenter which produces typical colonies on agar medium.

Salmonella species which are non-lactose fermenters and comprise many important
pathogenic species.

Shigella species which are non-lactose fermenting and have four pathogenic members.

Vibrio cholerae the causative agent of cholera which can produce outbreaks of disease.

Campylobacter and Helicobacter species which are often described as the curved Gram
negatives.

Pseudomonas species often recognised by their pigmentation.

Recognise API 20E kit
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Faculty of Medicine
King Abdul-Aziz University
At the end of the Parvobacteria session the student should be able to:
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Enumerate the six genera included in the group Parvobacteria.
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Mention the two members of the group which require blood for growth.
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Describe the microscopic and cultural characteristics of all members of the group.
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Discuss in detail the confirmatory tests used for the identification of Haemophilus
species.
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Describe briefly the confirmatory tests used for Bordetella and Brucella species.
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By using Zeihl-Neelse stain: Mycobacteria appear as acid-fast bacilli (AFB)
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Culture of Mycobacterim tuberculosis :
o on special media e.g Lowenstein-Jensen Medium
o The growth of Mycobacterim tuberculosis is very slow (6-8 weeks)
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Mycobacterim leprae can not be grown on laboratory media
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E.coli, is a normal inhabitant in the intestine of man and animals, sometimes may
produce disease. It produces distinctive colonies on MacConkey agar, XLD and
EMB agar. Confirmatory tests include biochemical tests.
Klebsiella species may be found also in the intestine of humans. Some species
produce disease. These are easily recognised as mucoid colonies on MacConkey agar.
Biochemical tests may be done for confirmation.
Proteus species also found as normal faecal flora can produce urinary tract infection.
They are identified in the laboratory by microscopy and culture. Typical colonies
show swarming and may be confirmed by biochemical identification tests.
The genus Salmonella has many pathogenic members; S. typhi produces enteric fever
and S. enteritidis the causative agent of food poisoning. After microscopy and culture
confirmation of Salmonella is performed by biochemical tests and slide
agglutination tests. In cases of typhoid blood culture is important in the first week of
illness and antibodies can be detected between day 7 and 10 by using an agglutination
test.
The genus Shigella includes S. dysenteriae which produces bacillary dysentery.
Laboratory diagnosis includes microscopy, culture and biochemical tests.
Diagnosis of cholera is important during epidemics and in endemic areas. Tests
include microscopy, culture, biochemical identification and agglutination tests.
The curved Gram-negatives Campylobacter and Helicobacter are identified
traditionally by microscopy and culture. Confirmatory tests include biochemical tests
and for Helicobacter ELISA tests and PCR methods may be used. Pseudomonas
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Phase II
107
Medical Microbiology
Faculty of Medicine
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King Abdul-Aziz University
species may be identified initially on culture by the production of the exo-pigment
followed by biochemical identification.
Commercial kits (API 20E) for biochemical tests are available for rapid and easy
identification of most members of the Enterobacteria.
The genus Haemophilus produces many important infections. Haemophilus
influenzae type b produces life threatening infections in young children. Laboratory
diagnosis of Haemophilus influenzae involves the use of microscopy and culture.
Haemophilus grows best on chocolate agar as it is a haemophilic organism.
Confirmatory tests for Haemophilus influenzae include the use of X and V factor
discs on nutrient agar and satellite phenomenon with S. aureus. Latex agglutination
tests are available and commonly used. Other confirmatory tests include the Quellung
reaction, FTA and CIE.
Diagnosis of Bordetella pertussis requires special samples such as either a pernasal
swab or cough plate. On selective agar B .pertussis produces mercury drop colonies
which may be confirmed using serological agglutination tests.
Brucellosis is often diagnosed clinically but requires confirmation by laboratory tests.
The best sample for diagnosis is blood which is cultured. The serum is used for
serological tests to see the rise in titre of antibodies using standard agglutination
test is diagnostic.
Legionella also a member of the Parvobacteria is more difficult to detect by
conventional microscopy and culture methods. Numerous new techniques have been
developed for it’s diagnosis which include a Urine antigen test and other serological
tests.
Yersinia (a member of Enterobacteriacae) and Fransicella are extremely hazardous
organisms. These require special safety precautions and are only cultured in
specialised laboratories.

Microbiology by Harvey, Champe and Fisher , Second Edition (2007). Publisher:
Lippincott Williams & Wilkins

Mackie and McCartney. Practical Medical Microbiology.
Phase II
108
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Practical 9:
Spirochaetes & Mycology
TUTOR:
Department: Medical Microbiology
SUMMARY:
 Spirochaetes are spiral in shape.
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Candida is a yeast which often found as normal flora in the oral cavity,
gastrointestinal tract and genital tract of humans. Candida albicans acts as an
opportunist pathogen which can produce a variety of clinical infections. This
practical session will mainly deal with Candida but students will be expected to be
familiar with other techniques used in mycology.
OBJECTIVES:
At the end of this session the student should be able to:
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Describe the appearance of Borrelia vinviti (Gram-negative spiral rods)
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Describe the main characteristics of yeasts.
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Describe the agar media used for culture of fungi.
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Mention the confirmatory tests used for Candida albicans.
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Have theoretical knowledge on the diagnostic methods used for diagnosis of moulds
which produce superficial and dermatophyte infections.
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Discuss briefly diagnostic methods used for diagnosis of systemic fungal infections
produced mainly by dimorphic fungi.
o In Vincet' angina: Many spirochaetes of Borrelia vinviti (Gram-negative spiral rods)
and Fusobacteria are seen.
Phase II
109
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
o Candida albicans is a single cellular, oval or spherical organism. Mostly it shows
budding which is easily detected under the microscope. All fungi grow well on
Sabaroud agar and candida produces large colonies with a typical smell.
Confirmatory tests for candida include the production of chlamydospores on
cornmeal agar and the Germ tube test. Candida albicans can produce oral thrush,
vaginitis, alimentary and cutaneous candidiasis. In addition Candida can often
produce systemic infections. Fungi are important pathogens and fungal infections are
classified often according to the site that they affect. Diagnosis of superficial fungal
infections mainly involves collection of suitable specimens followed by microscopy
and culture. Systemic fungal diseases are diagnosed by microscopy and culture also
but have in addition numerous serological and skin tests available for confirmation.

Microbiology by Harvey, Champe and Fisher , Second Edition (2007). Publisher:
Lippincott Williams & Wilkins

Mackie and McCartney. Practical Medical Microbiology.
Phase II
110
Medical Microbiology
Faculty of Medicine
King Abdul-Aziz University
Practical 10:
Virology
TUTOR:
Department: Medical Microbiology
SUMMARY:
For viral infections, rapid diagnosis is made by electron microscopy, serology, and PCR.
However, isolation by growing in tissue culture, embryonated eggs, or in animal is time
consuming but more sensitive and conclusive method.
OBJECTIVES:
At the end of this session the student should be able to:
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Describe basic methods used for the laboratory diagnosis of viral diseases.
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Slide demonstration for laboratory diagnosis of viral diseases.

Microbiology by Harvey, Champe and Fisher. Second Edition (2007). Publisher:
Lippincott Williams & Wilkins

Mackie and McCartney. Practical Medical Microbiology.
Phase II
111
Medical Microbiology